John Calvin Commentary Psalms 41:4

"I said, O Jehovah, have mercy upon me: Heal my soul; for I have sinned against thee." — Psalms 41:4 (ASV)

I have said, O Jehovah! have mercy upon me. By this verse he shows that in his adversity he did not seek to soothe his mind with flattery, as most people do, who try to lessen their sorrows with some empty consolation. And certainly, the person who is guided by the Spirit of God will, when warned by God through the afflictions they experience, frankly acknowledge their sins, and quietly submit to the admonitions of fellow believers; indeed, they will even anticipate them with a voluntary confession.

David here sets forth a mark by which he distinguishes himself from the reprobate and wicked, when he tells us that he earnestly pleaded that his sin might not be counted against him, and that he had sought refuge in the mercy of God. He indeed requests that some alleviation might be granted to him from the affliction he endured; but he rises to a higher source of relief when he asks that through the forgiveness of his sins he might obtain reconciliation with God.

Those who seek a remedy only for the outward miseries they suffer, while all the time neglecting their cause, invert the natural order of things, as we have said elsewhere. They act like a sick man who seeks only to quench his thirst but never thinks of the fever from which he suffers, and which is the chief cause of his trouble.

Before David, therefore, speaks at all of the healing of his soul, that is to say, of his life, he first says, Have mercy upon me: and with this we must connect the reason which immediately follows—for I have sinned against thee. In saying this, he confesses that God is justly displeased with him, and that he can only be restored to God's favor by his sins being blotted out.

I take the particle כי, ki, in its proper and natural meaning, and not in an opposing sense, as some would understand it. He asks then that God would have mercy upon him because he had sinned. From that proceeds the healing of the soul, which he places between his prayer and confession as the effect of God's compassion and mercy; for David expects that as soon as he has obtained forgiveness, he will also obtain relief from his affliction.