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How did they keep their bloodlines disease free if they mated?

It has often been stated in articles that Egyptian pharoahs "married their sisters" but that is a misleading oversimplification. The practice was actually limited to a very specific relationship in which they had the same father but different mothers, i.e. half-sister and half-brother.

There is some interesting discussion of this practice (which was not limited to Egypt but occurred in other ancient middle-eastern dynasties as well) in the works of Zechariah Sitchin. His thesis was that the practice actually strengthened the bloodlines of the royal classes of these kingdoms because of their "unique" geneological heritage. That's a discussion for another time, however. /grin

Another example of this is found in the Old Testament account of Abraham marrying his sister Sarah. The original form of the name Abraham was "Abram", which was Sumerian, and Sarah was "Sarai" which was Sumerian for "princess". Thus Abraham and Sarah were expatriate Sumerian royalty from the city of Ur, who were simply following the traditional practice of their culture.

How did they keep their bloodlines disease free if they mated?

The close relation of parents is not a gurantee of defects. In fact, sometimes not only do they not have defects, but they may have above average positive traits. However, the marriage of close relations does increase the chances of bringing out recessive traits which can cause problems. In antiquity as today, sometimes the children of these marriages had problems and sometimes they did not. In the case of Tutankhamen, two stillborn baby girls were found buried with him in the tomb. They are almost certainly his own children.

Who sez they kept them disease free? ;') Akhenaten (Tut's father?) appears to have suffered from Marfan's syndrome, and judging from the Amarna-period art, so did his offspring. His offspring were frail. Also, there were some pharaohs who came from nowhere, and were apparently military leaders, or from the priesthood(s), chosen apparently because the line of pharaohs finally inbred itself out of existence.

Each pharaoh had to come from "the same womb" as his predecessor, which led to incestuous marriages, and there's no way to disguise it. Fathers married daughters, uncles nieces, brothers sisters, and of course, cousins married. Not all of these unions produced offspring, and favorite sons were put on the throne, and married to a princess of the blood just to legitimize the reign -- although I'm not an advocate for the legitimacy of a monarchy.