Objection 1. It would seem that original sin is more in the flesh than in the soul. Because the rebellion of the flesh against the mind arises from the corruption of original sin. Now the root of this rebellion is seated in the flesh: for the Apostle says (Romans 7:23): "I see another law in my members fighting against the law of my mind." Therefore original sin is seated chiefly in the flesh.
Objection 2. Further, a thing is more in its cause than in its effect: thus heat is in the heating fire more than in the hot water. Now the soul is infected with the corruption of original sin by the carnal semen. Therefore original sin is in the flesh rather than in the soul.
Objection 3. Further, we contract original sin from our first parent, in so far as we were in him by reason of seminal virtue. Now our souls were not in him thus, but only our flesh. Therefore original sin is not in the soul, but in the flesh.
Objection 4. Further, the rational soul created by God is infused into the body. If therefore the soul were infected with original sin, it would follow that it is corrupted in its creation or infusion: and thus God would be the cause of sin, since He is the author of the soul's creation and fusion.
Objection 5. Further, no wise man pours a precious liquid into a vessel, knowing that the vessel will corrupt the liquid. But the rational soul is more precious than any liquid. If therefore the soul, by being united with the body, could be corrupted with the infection of original sin, God, Who is wisdom itself, would never infuse the soul into such a body. And yet He does; wherefore it is not corrupted by the flesh. Therefore original sin is not in the soul but in the flesh.
On the contrary, The same is the subject of a virtue and of the vice or sin contrary to that virtue. But the flesh cannot be the subject of virtue: for the Apostle says (Romans 7:18): "I know that there dwelleth not in me, that is to say, in my flesh, that which is good." Therefore the flesh cannot be the subject of original sin, but only the soul.
I answer that, One thing can be in another in two ways. First, as in its cause, either principal, or instrumental; secondly, as in its subject. Accordingly the original sin of all men was in Adam indeed, as in its principal cause, according to the words of the Apostle (Romans 5:12): "In whom all have sinned": whereas it is in the bodily semen, as in its instrumental cause, since it is by the active power of the semen that original sin together with human nature is transmitted to the child. But original sin can nowise be in the flesh as its subject, but only in the soul.
The reason for this is that, as stated above (Question 81, Article 1), original sin is transmitted from the will of our first parent to this posterity by a certain movement of generation, in the same way as actual sin is transmitted from any man's will to his other parts. Now in this transmission it is to be observed, that whatever accrues from the motion of the will consenting to sin, to any part of man that can in any way share in that guilt, either as its subject or as its instrument, has the character of sin. Thus from the will consenting to gluttony, concupiscence of food accrues to the concupiscible faculty, and partaking of food accrues to the hand and the mouth, which, in so far as they are moved by the will to sin, are the instruments of sin. But that further action is evoked in the nutritive power and the internal members, which have no natural aptitude for being moved by the will, does not bear the character of guilt.
Accordingly, since the soul can be the subject of guilt, while the flesh, of itself, cannot be the subject of guilt; whatever accrues to the soul from the corruption of the first sin, has the character of guilt, while whatever accrues to the flesh, has the character, not of guilt but of punishment: so that, therefore, the soul is the subject of original sin, and not the flesh.
Reply to Objection 1. As Augustine says (Retract. i, 27) [Cf. QQ. lxxxiii, qu. 66, the Apostle is speaking, in that passage, of man already redeemed, who is delivered from guilt, but is still liable to punishment, by reason of which sin is stated to dwell "in the flesh." Consequently it follows that the flesh is the subject, not of guilt, but of punishment.
Reply to Objection 2. Original sin is caused by the semen as instrumental cause. Now there is no need for anything to be more in the instrumental cause than in the effect; but only in the principal cause: and, in this way, original sin was in Adam more fully, since in him it had the nature of actual sin.
Reply to Objection 3. The soul of any individual man was in Adam, in respect of his seminal power, not indeed as in its effective principle, but as in a dispositive principle: because the bodily semen, which is transmitted from Adam, does not of its own power produce the rational soul, but disposes the matter for it.
Reply to Objection 4. The corruption of original sin is nowise caused by God, but by the sin alone of our first parent through carnal generation. And so, since creation implies a relation in the soul to God alone, it cannot be said that the soul is tainted through being created. On the other hand, infusion implies relation both to God infusing and to the flesh into which the soul is infused. And so, with regard to God infusing, it cannot be said that the soul is stained through being infused; but only with regard to the body into which it is infused.
Reply to Objection 5. The common good takes precedence of private good. Wherefore God, according to His wisdom, does not overlook the general order of things (which is that such a soul be infused into such a body), lest this soul contract a singular corruption: all the more that the nature of the soul demands that it should not exist prior to its infusion into the body, as stated in the I, 90, 4; I, 118, 3. And it is better for the soul to be thus, according to its nature, than not to be at all, especially since it can avoid damnation, by means of grace.
Source: Summa Theologica (New Advent)