59 Saint Paul does not merely acknowledge that conscience acts as a "witness"; he also reveals the way in which conscience performs that function. He speaks of "conflicting thoughts" which accuse or excuse the Gentiles with regard to their behaviour (cf. Rom 2:15). The term "conflicting thoughts" clarifies the precise nature of conscience: it is a moral judgment about man and his actions, a judgment either of acquittal or of condemnation, according as human acts are in conformity or not with the law of God written on the heart. In the same text the Apostle clearly speaks of the judgment of actions, the judgment of their author and the moment when that judgment will be definitively rendered: "(This will take place) on that day when, according to my Gospel, God judges the secrets of men by Christ Jesus" ( Rom 2:16). The judgment of conscience is a practical judgment, a judgment which makes known what man must do or not do, or which assesses an act already performed by him. It is a judgment which applies to a concrete situation the rational conviction that one must love and do good and avoid evil. This first principle of practical reason is part of the natural law; indeed it constitutes the very foundation of the natural law, inasmuch as it expresses that primordial insight about good and evil, that reflection of God's creative wisdom which, like an imperishable spark ( scintilla animae ), shines in the heart of every man. But whereas the natural law discloses the objective and universal demands of the moral good, conscience is the application of the law to a particular case; this application of the law thus becomes an inner dictate for the individual, a summons to do what is good in this particular situation. Conscience thus formulates moral obligation in the light of the natural law: it is the obligation to do what the individual, through the workings of his conscience, knows to be a good he is called to do here and now. The universality of the law and its obligation are acknowledged, not suppressed, once reason has established the law's application in concrete present circumstances. The judgment of conscience states "in an ultimate way" whether a certain particular kind of behaviour is in conformity with the law; it formulates the proximate norm of the morality of a voluntary act, "applying the objective law to a particular case".
Source: Veritatis Splendor (Vatican.va)