There is more than one reason.
Sickle-cell Anemia is an example where natural selection made it more prevalent than it would naturally be. Normal blood cells are caused by a gene that has incomplete dominance. If the normal gene and sickle gene are present some of the red blood cells will be normal and some will be sickled. Natural selection bred this out of people who lived in temperate climates, but not in tropical climates. In tropical climates, Malaria was a common ailment, and having a mix of normal and sickled red blood cells hinders the progression of Malaria, thus making the gene's presence advantageous.
Inbreeding is another cause. In insular populations (i.e. those that rarely mix with others), frequently cousins and other extended relatives intermarry. This encourages recessive traits, which are the source of several genetic diseases, to be present in both parents, increasing the likelihood of a child born with the condition, and if that child parents a child of their own, the child will either have the condition, or be a healthy carrier, which leads to future generations having carriers, and thus more risk.
Geographic mutation is yet another cause. Some illnesses are caused by mutations resulting from exposure to factor specific to location. Idaho downwinders are an example of this. Because these people lived downwind from above ground Nuclear tests in the 50s and 60s, they now have a higher prevalence of cancers related to radiation exposure, and these cancers are caused by genetic mutations resulting from the radiation.