The human endogenous retroviruses HERV-K113 and HERV-K115 are full-length proviruses but unusual in being found in only a proportion of the population. Here, we study the geographic distribution of these HERVs and their prevalence in autoimmune disease. The frequency of HERV-K113 and HERV-K115 in 174 individuals from Africa was 21.8 and 34.1%, respectively, compared to 4.16 and 1% in 96 people in the United Kingdom (p < 0.001). Prevalence in Yemen (n = 56) was 8 and 7.14% and in Papua New Guinea (n = 54) 0% for both. In the United Kingdom, HERV-K113 was found in 15.6% of 96 Sjögren's syndrome patients (p < 0.01) and 11.9% of 109 multiple sclerosis patients (p < 0.05). No increase in prevalence in either disease was seen with HERV-K115. These data suggest that both viruses are recently integrated and/or under positive evolutionary selection pressure. HERV-K113 may be a genetic risk factor for some types of autoimmunity.