From the close family relationships in Egyptian mythology and the fact that Egyptians seemed to have no taboo against incest, many have concluded that incest was rife in ancient Egypt.
There were probably some brother and sister marriages, but more likely than not, the siblings in question would have been half-brothers and half-sisters. The problem arises from the limited Egyptian terms of kinship, which are very confusing. A 'father' could refer to the actual father, the grandfather or male ancestors, while 'mother' could be the same, but for the females of the family. 'Sister' could mean a lover, a wife, a mistress or concubine, niece or aunt!
The royal family, on the other hand, did have more incestuous marriages. The royal blood ran through the females, not the males. To become pharaoh, a man had to marry a royal princess... which would be his sister or half-sister.
The prevalence of brother-sister marriages within the New Kingdom royal family, a custom in obvious contrast to contemporary non-royal marriage patters, appears to have been an attempt to reinforce the links between the royal family and the gods who themselves frequently indulged in brother-sister unions.