Whom did Cain marry? If it was his sister, then in Leviticus 20:17 it is written, that one cannot marry his own sister. So how can Cain's marriage be lawful?
The Bible is silent about who Cain's wife was. Looking at the possible options, it has to be his sister. Let us analyze and see the other possibilities first.
If God had to create a wife for Cain, as He created Eve for Adam, she would have been an unfallen woman (i.e., a sinless person). And an unfallen woman cannot marry a fallen man. That would be tremendously unfair if God did it. And on the other hand God will not create a sinner to give Cain his wife, as God makes only perfect things. So creating a wife for Cain was impossible. (And so was it for that generation.)
If God did not permit Cain to marry his sister, then there would be only one generation of people-Just Adam and Eve's children, and no further. And the human race would have come to an end a little after the death of our first parents!
So Cain had to marry his own sister, for God permitted it then, as the human race had to populate the earth. (Please remember it was an exceptional case, as there were no other women for Cain to marry, except one of his sisters.)
That does not mean if it was okay then, it is okay even now. For no one is in Cain's position today. There are several choices for all to choose from.
The law is clear in the book of Leviticus, which states:
And if a man shall take his sister, his father's daughter, or his mother's daughter, and see her nakedness, and she see his nakedness; it is a wicked thing; and they shall be cut off in the sight of their people: he hath uncovered his sister's nakedness; he shall bear his iniquity. (Leviticus 20:17)
ONE MIGHT SAY: Wasn't God changing His Word by permitting one generation to do it and forbidding later generations? No, not at all! There is no inconsistency in it. A few illustrations will make it clear that this pattern was not unique.
Think of the traffic laws. One is not permitted to cross the stoplight, and also to over speed. But don't ambulances and police vehicles do this many a time? And it is lawful! Can anyone rightly accuse them of being lawbreakers? Imagine the plight, if ambulances were not allowed to over speed, and sometimes by-pass the stoplight. Many patients would have died before reaching the hospitals.
And on occasions if the police vehicles cannot over speed or jump the stoplight, many offenders would escape. So there is room for special cases everywhere. And it is within the law!
When a civilian kills another man it is called murder, and the law of the land punishes him; but when a soldier kills an enemy soldier, he is hailed as patriotic! And the law of the land does not punish him, but rather it commands him to do so whenever needed.
Look at the Fourth Commandment for instance. Working on any of the six days is lawful, but the same secular work done on the seventh day is unlawful (See Exodus 20:8-11). Can anyone accuse God of not being consistent all seven days? Well, that is the rule--Six days work is legal, but secular work on the seventh day is illegal and unlawful in God's sight.
The same way, for Cain (and his generation) to marry his sister was legal, but for anyone else thereafter to do that, becomes illegal and unlawful!
God is the law Giver, and God is the law Definer. None can interpret it better than Him. His Word is truth!
So Cain marrying his sister was lawful. And it would not affect, medically, their children, because that generation was nearly perfect as their parents came forth fresh from the Master's own hands!