Human endogenous retroviruses (HERVs) expression has been suspected as a factor participating in the development of autoimmune diseases. Employing the dot blot hybridisation, we observed that 90.9% of mixed connective tissue disease (MCTD) (n = 22) patients exhibited the presence of human immunodeficiency virus type 1 (HIV-1) conserved pol sequence in DNA isolated from serum. The same investigation conducted in the group of systemic sclerosis (SSc) (n = 79) patients identified a conserved retroviral pol sequence in 34.6% of antinuclear antibodies (ANA) positive (n = 52) and 40.7% of ANA negative (n = 27) patients. However, 100% of anti-U1-ribonucleoprotein (RNP) positive SSc (n = 9) patients exhibited the presence of HIV-1 conserved pol sequence. Our findings suggest that the presence of retroviral sequence in serum of MCTD and SSc patients may correlate with development of autoimmune response directed against U1-70 kDa polypeptide antigen.