Abstract It has been reported that more male DNA of presumed fetal origin is present in the blood and skin of women with systemic sclerosis (SSc) as compared with healthy controls after delivery, but these findings are controversial. We sought to determine whether male cell DNA is present in SSc using a quantitative polymerase chain reaction for Y chromosome DNA. The study groups comprised 57 healthy women, 49 patients with SSc and 30 patients with connective tissue diseases other than SSc who had given birth to at least one son and/or had experienced fetal loss. The intensity of the PCR bands on negatives of gel photographs was quantified with a video densitometer linked to a computer analysis system. Positive Y chromosome DNA was found in 20 healthy women, 14 SSc patients and 6 patients with connective tissue diseases other than SSc. The occurrence rate of DNA equivalents of male cells among the three groups showed no significant differences. The number of male cell DNA equivalents per 80 ng tissue DNA in SSc patients (4.59 ± 9.63), however, was significantly higher than in healthy women (1.83 ± 4.96; P < 0.05) and in patients with connective tissue diseases other than SSc (0.27 ± 0.64; P < 0.01). The occurrence rate of fetal loss in male cell DNA-positive SSc (eight) was significantly higher than in male cell DNA-negative SSc patients (four; P < 0.01). No correlation was found between the number of male cell DNA equivalents and birth of sons or clinicolaboratory findings. These results indicate that the elevated amount of male cell DNA in SSc skin tissue may contribute to the pathogenesis of SSc.