Conscience at the Crossroads

On Informed Conscience, Faithful Dissent, and the Path of Integrity

Photo by Jens Lelie on Unsplash

As one might expect, my ongoing journey of deconstruction as a priest has involved some tense, difficult conversations with Church authorities. In one recent conversation with my bishop, I asked him what someone like me is supposed to do, when his conscience and the Church’s teaching seem to pull in opposite directions.

His answer was careful, almost rehearsed. “Well, of course, we must always follow our conscience,” he said. “But that conscience has to be informed.”

It was a telling moment. On the surface, we agreed. The Church has always taught that the judgment of one’s conscience is sacred and binding. One must never be made to violate their conscience, even if that judgment turns out to have been mistaken in a particular case. And yet, in practice, this strong affirmation often comes with a little asterisk: you may follow your conscience … so long as it tells you to do what the Church already teaches. It’s a bit like Henry Ford’s famous quote: “You can have any color you want, as long as it’s black.”

That quiet qualification is no small thing. It suggests that the process of “informing” one’s conscience is less a process of genuine moral discernment than a march toward a predetermined destination. It implies that a truly well-formed conscience is one that ultimately agrees with each and every teaching of the Church. And if your conscience hasn’t yet arrived at such serene submission to the Church’s judgments, well, you must not be done forming it yet. Keep going until you come to the right conclusions.

But what if conscience is not, in fact, a closed-loop system? What if it’s something far deeper, holier, and riskier than that? What if, in fact, conscience is the very sanctuary of the soul where God whispers to us in a “still, small voice,” not to rubber-stamp each teaching of the Roman congregations, but to call us into greater integrity and holiness of life? What would happen if we had the courage to follow that voice honestly and prayerfully, even when it leads us somewhere the Church isn’t yet ready to go?

In this post, I want to explore the idea of conscience and its role in the moral life. Drawing, as ever, from the theological sources of our Catholic tradition, we’ll examine what conscience really is, how it is formed, and what it means to follow it faithfully, especially as LGBTQ+ Catholics. We’ll consider how the Church’s teaching authority on matters of faith and morals can coexist with the real authority of conscience, and what it means, in practical and pastoral terms, to listen for the Shepherd’s voice when it comes, not from the pulpit, but from within the deepest center of our souls.

What Is Conscience?

In popular parlance, conscience is often equated with a kind of moral feeling or inner sense of having done right or wrong. A boy might return a candy bar he swiped from the supermarket because he had a “guilty conscience.” Another person might go to confession after speeding on the freeway, certain that they’ve committed a mortal sin, only to be told by their priest that they are afflicted with a “sensitive conscience.” On the other hand, someone experiencing a sense of moral peace after a difficult decision could say with St. Paul, “My conscience is clear” (1 Corinthians 4:4 NIV).¹

This common definition of conscience is not wrong, but it is incomplete. Theologically speaking, conscience is far more than a feeling, a mood, a tendency, or even a moral opinion. According to the Catechism of the Catholic Church, conscience is “man’s most secret core and his sanctuary. There he is alone with God, whose voice echoes in his depths.”² Conscience is that interior place where we encounter the living God, calling us to love, to do good, and to avoid evil. It is “the aboriginal Vicar of Christ,” as Cardinal John Henry Newman famously wrote,³ not speaking ex cathedra from the Chair of Peter, but ex cordis, from His throne in the human heart.

Yet conscience is not infallible, as anyone who has spent long observing human behavior (or examining their own) can readily attest. St. Thomas Aquinas distinguished between two related but distinct aspects of conscience: synderesis, the innate habit or disposition of the human intellect to grasp the basic principles of the moral law (e.g. “do good, avoid evil”), and conscientia, the concrete judgment of practical reason about what we must do in a given situation.⁴

According to the Thomistic system, synderesis is our natural inclination toward the good. It is stable, universal, and infallible in its orientation. It cannot be lost. Conscientia, on the other hand, is the act of applying the basic moral principles discovered by synderesis to specific circumstances. Because this judgment involves contingent knowledge, subjective interpretation, and moral deliberation, it can err.

Still, Aquinas insisted, even a mistaken judgment of conscience is binding. If someone sincerely believes an action to be evil, then choosing to do it constitutes a sin for that person, even if the act itself is objectively neutral, or even good. To act against conscience is always to act against one’s own best understanding of God’s will.⁵

While the Thomistic understanding emphasized conscience as the rational application of moral knowledge, twentieth-century theologians have increasingly highlighted the existential and relational dimensions of conscience. Rather than viewing it solely as a rational faculty of moral decision-making, conscience becomes an expression of the whole person in their unfolding relationship with truth and the highest human values. As moral theologian Seán Fagan writes, “It is a misleading metaphor to speak of a person ‘having a conscience.’ The reality is that one is a conscience.”⁶ Conscience is the person’s entire interior orientation toward authenticity and truth.

In this sense, conscience is deeply personal, but never merely private. It is the seat of our response to grace. It is where the Word of God becomes flesh in our actual moral decisions. It is how the Holy Spirit teaches us, not only what is permitted, but what is worthy of the kind of people we are becoming .

This is precisely why conscience cannot be reduced to conformity. As Fagan notes, “The conscience which most fully carries moral authority … is the conscience which is continually self-critical, aware of the dangers of ignorance, bias, prejudice, selfishness, arrogance, and self-sufficiency.”⁷ A conscience worth trusting is not one that parrots the predetermined judgments of others, but one formed in humility and oriented toward truth, constantly gathering new insights, receiving correction, and seeking to purify its own judgments, even when this is uncomfortable.

In fact, the judgment of conscience may be most authoritative when it’s uncomfortable. James Alison puts it this way: “Conscience kicks in when something we might do could seriously rewrite the story of who we are.”⁸ For many LGBTQ+ Catholics, that moment comes when we begin to wrestle with the real moral questions of our sexual identity, relationships, and the possibility of love: Is this who I am? Is this how I’m meant to love? Can this be good?

Of course, conscience rarely gives a quick or easy answer to such questions. It doesn’t offer shortcuts through the complexities of moral decision-making. What it does offer—if we have the courage to listen—is the possibility of integrity. Of truthfulness. Of standing before God, even when the conclusions we’ve come to don’t fit into the standard categories we’ve been given, and saying with St. Paul: “My conscience is clear.”

How Is Conscience Formed?

If conscience is the sacred interior space where God speaks to the heart, calling us to truth, to goodness, and to love, then the formation of conscience must be something more than simply memorizing the rules. Unfortunately, that’s how it is often presented, especially in more fundamentalist Catholic circles. “Formation” is reduced to a process of aligning one’s inner sense of right and wrong with the external teachings of the Church, until there’s no longer any tension between the two.

The Church’s own tradition affirms a much more dynamic and complex process. First of all, according to the Catechism, the formation of conscience is not optional: “Conscience must be informed and moral judgment enlightened.”⁹ This formation is a lifelong task,¹⁰ one which involves not only education in doctrine, but engaging with a range of sources and practices that foster spiritual and moral maturity:

• The Word of God, taken to heart through faith and prayer;

• The witness and advice of others, especially “competent people” (CCC §1788);

• The authoritative teaching of the Church, which serves as a “guide,” not a substitute, for moral discernment;

• The gifts of the Holy Spirit, particularly wisdom, counsel, and understanding, and

• The discipline of self-examination, critically considering one’s own motives and desires in the light of Christ and His Cross.¹¹

Clearly, then, to form one’s conscience is not simply to download doctrine into the mind until it is wearied into submission. It is a process of holistic development, aimed at becoming the kind of person who can perceive, desire, and respond freely to the good, making a “responsible decision in accord with reasonable judgment.”¹² Formation is not merely a matter of conforming to an external standard, but of growing into moral adulthood, cultivating the moral freedom and interior responsibility required to follow the truth wherever it leads.

How Do We Recognize an Authentic Judgment of Conscience?

If we grant that the task of conscience formation involves more than just conforming to predetermined conclusions, then the question arises: How do we know when a judgment of conscience is trustworthy? What distinguishes an authentic moral judgment from mere rationalization or self-deception?

First and foremost, the authentic judgment of conscience is marked by a sincere, interior commitment to truth and love. This sincerity is not a vague emotional state, but a disposition of openness to reality as it is, not merely as we might wish it to be. According to Veritatis Splendor, “conscience does not create moral law; it bears witness to a moral law which has its origin in God.”¹³ An authentic act of conscience, then, is one that seeks not to justify what is convenient, but to uncover what is truly good.

This judgment is always shaped by the moral virtues, especially prudence, humility, and responsibility. It is discerning and reflective rather than reactive. It does not rush to resolve tension, but holds space for complexity, ambiguity, and growth. It asks, What is the truth of this situation? What does love require of me here?

Practically speaking, the tradition has identified several signs of trustworthy moral discernment, which may be applied here to recognize an authentic judgment of conscience. These include:

• A desire for the good of others, not just one’s own peace or convenience;¹⁴

• Coherence across time, rather than a one-off decision to relieve an immediate tension;¹⁵

• A willingness to submit the judgment to dialogue, spiritual direction, and external structures of accountability;¹⁶ and often

• A deepening sense of peace and consolation—not emotional ease, perhaps, but growing interior integration, clarity, and resolve.¹⁷

None of these signs is definitive on its own, but together, they suggest a pattern. An authentic judgment of conscience should enable the person to stand before God and others with a sense of peace and integrity, even—or perhaps especially—when that judgment is costly, misunderstood, or at odds with current teaching.

This is especially vital in areas where the current doctrine is contested or still in development. The Second Vatican Council reminded us that “in the depths of his conscience, man discovers a law which he has not laid upon himself but which he must obey.”¹⁸ That law is not reducible to ecclesial doctrines. It emerges through grace, through prayerful discernment, and the gradual unfolding of each person’s life in relationship to God.

To be clear, this does not mean every conclusion of conscience is correct. The Church acknowledges that conscience can err. However, as James Alison observes, the question we must ask ourselves is not “Is my conscience infallible?” (it’s not), but rather, “Is it honest? Is it grounded in reality? Is it becoming more attuned to love, truth, and grace?” The measure is not perfection, but fidelity.

Ultimately, even if one’s conscience is mistaken, the obligation remains. One must follow their conscience. To do otherwise is to sin, because it is to act against what one believes to be right.¹⁹ Of course, the more serious the matter, the more rigorous the discernment must be. But even in uncertainty, a person must listen to the voice of conscience, discern the right course of action, and finally, respond—not with predetermined conclusions, but with the honesty and integrity demanded of one who stands as a free moral agent before the living God.

What Do We Do When Teaching and Discernment Diverge?

What happens when the sincere, prayerful judgment of conscience leads a person to a conclusion that diverges from official Church teaching?

This is not a hypothetical question, of course. It is a lived reality for me, as it is for many faithful Catholics. James Alison observes that LGBTQ+ Catholics, in particular, often come to recognize the goodness and truth of their own identity, not through external approval or affirmation, but through the long, painful process of coming at last to a judgment of conscience.²⁰

More and more LGBTQ+ Catholics have discovered, through the careful discernment of conscience—and contrary to the official teaching of the Church—that their capacity to love someone of the same sex is not an obstacle to holiness, but part of their path toward it. In this light, the teaching that calls their orientation “disordered” begins to look less like the prophetic voice of tradition and more like the inertia of a fearful institution struggling to make sense of lives it does not yet understand.

Of course, it is not surprising that many LGBTQ+ Catholics who come to this conclusion leave the faith or disaffiliate in some measure from the institution of the Church. Even if they wish to continue practicing the Catholic faith, it is difficult to exist in a space which calls your very identity, or more specifically the “tendency” that defines it, “objectively disordered,” once you have deconstructed that teaching and come to a conclusion opposed to that of the Magisterium.

Amoris Laetitia, Pope Francis’s 2016 exhortation on family life, may suggest a way forward for Catholics who find themselves in situations like this. In paragraph 303, the late Holy Father wrote:

“Conscience can do more than recognize that a given situation does not correspond objectively to the overall demands of the Gospel. It can also recognize with sincerity and honesty what for now is the most generous response which can be given to God, and come to see with a certain moral security that it is what God himself is asking.”²¹

This vision of conscience stands within a long and venerable tradition of recognizing the primacy of conscience, even when it leads a person into conflict with external authority. When one makes the most generous response one can to the demands of love, having discerned this response with sincerity and honesty, one can move forward with a “certain moral security that it is what God himself is asking,” whatever other voices might say.

Such a vision also implicitly reframes the role of ecclesial authority. Rather than being positioned above conscience as judge and arbiter, the Church’s moral teaching becomes a reference point, a guide, and a companion in discernment, as Pope Francis pointedly remarked in the same encyclical: “We have been called to form consciences, not to replace them.”²²

Moral theologian Rudolf Hoffmann states this principle clearly: “The judgment of conscience is the ultimate definitive norm for the individual.”²³ Of course, this is not giving license to relativism or self-will. It simply acknowledges that moral agency cannot be outsourced. No Roman congregation, no superior, no external authority at all can take the place of conscience. Doctrine may teach; tradition may guide; authorities may instruct, but in the end, it is the person who must answer for their own soul.

And when a queer person, through sincere discernment and prayer, recognizes that love—real, committed, self-giving love—has taken root in their life, the question is no longer whether that love fits a theological category. The question is whether they will be faithful to the truth they have come to know.

The Vicar Within

The voice of conscience is rarely loud. It does not shout to be heard. Like the still, small voice that came to Elijah in the cave (1 Kings 19:12), the voice of conscience often speaks quietly, buried beneath many layers of fear, shame, and the pressure to conform. Yet even there, in the depths, it is the voice that dares to ask not only what is allowed, but what is loving. Not only what is expected of us, but what is true.

Hearing and following that voice is not easy. It requires courage, humility, and discernment. And it can feel like walking out ahead of the Church, unsure if anyone will follow.

It consoles me to know that this, too, is part of our tradition. St. Joan of Arc was burned at the stake for obeying a voice she could not deny. They thought she was a witch; she turned out to be a mystic. St. Thomas More went to the scaffold because he could not in good conscience affirm what he believed to be false. They said he was a traitor; he proved himself a martyr. St. Catherine of Siena rebuked the Pope himself, urging him to return to Rome, because of her unwavering obedience to the voice of Christ she heard within her soul. And in our own time, Christian leaders like Martin Luther King Jr. have shown that fidelity to conscience can be the greatest witness to the power of the Gospel to transform the world.

The authentic voice of conscience is not in opposition to Christ. It is the echo of His voice speaking deep within us. As Newman wrote, conscience is the “aboriginal Vicar of Christ,” the first and most interior place where His lordship is known. And as many queer Catholics have found, it is in obeying that voice that we come to know God more deeply, more honestly, and more freely than ever before.

To follow conscience, then, is not to stand against the Church. It is to stand where Christ already is—at the margins, in the silence, calling us by name. And to walk this path with integrity is not to walk away from the Church. It is to walk ahead as witnesses, bearing light toward what the Church herself, in time, may come to recognize as truth.

1. The Holy Bible: New International Version (Grand Rapids: Zondervan, 2011).

2. Catechism of the Catholic Church, 2nd ed. (Vatican City: Libreria Editrice Vaticana, 1997), §1776, quoting Vatican Council II, Gaudium et spes, §16.

3. John Henry Newman, “Letter to the Duke of Norfolk” (1875), in Certain Difficulties Felt by Anglicans in Catholic Teaching, vol. 2 (London: Longmans, Green, and Co., 1890), 248.

4. Thomas Aquinas, Summa Theologiae, I, q. 79, aa. 12-13, trans. Fathers of the English Dominican Province (New York: Benziger Bros., 1947).

5. ST, I, q. 79, a. 13.

6. Seán Fagan, “Conscience,” in The New Dictionary of Theology, ed. Joseph A. Komonchak, Mary Collins, and Dermot A. Lane (Collegeville, MN: Liturgical Press, 2000), 228-230.

7. Fagan, “Conscience,” 229.

8. James Alison, “Conscience reveals to LGBTQ people who we really are,” Outreach, accessed July 26, 2023.

9. CCC, §1783.

10. CCC, §1784.

11. CCC, §1785.

12. Fagan, “Conscience,” 229.

13. John Paul II, Veritatis splendor (1993), §60.

14. CCC, §1789.

15. See St. Ignatius of Loyola, “Rules for the Discernment of Spirits” (First Week, Rule 5), in Spiritual Exercises, trans. Louis J. Puhl (Chicago: Loyola Press, 1951), 83.

16. CCC, §1785.

17. Jules Toner, A Commentary on Saint Ignatius’ Rules for the Discernment of Spirits (St. Louis: Institute of Jesuit Sources, 1982), 14–16.

18. Vatican Council II, Gaudium et spes, §16.

19. CCC, §§1790–1793.

20. Alison, “Conscience.”

21. Pope Francis, Amoris laetitia (2016), §303.

22. Amoris laetitia, §37.

23. Rudolf Hofmann, “Conscience,” in Sacramentum Mundi: An Encyclopedia of Theology, ed. Adolf Darlap (New York; London: Burns & Oates; Herder and Herder, 1968–1970), 411–414.