Microchimerism is defined as the presence of non-self and circulating cells in a host. The current study aimed to assess the effect of microchimerism on scleroderma major organ involvements. This cross-sectional study was conducted on 56 scleroderma patients registered in a tertiary rheumatology center of Shiraz University of Medical Sciences. Information on the patients' demographics and disease complications was gathered through a review of medical records. Skin score was applied to better assess skin thickening. High Resolution CT-scan as well as pulmonary function test (PFT) results were also used to investigate pulmonary involvement in patients. Y chromosome serum levels were measured using Phenol Chloroform Extraction protocol and following real-time PCR. Fifty-six scleroderma patients with a mean age of 46±10 years were recruited in this study (58.9% with diffuse scleroderma and 41.07% with limited scleroderma). Other than skin thickening, the most common clinical presentation among the patients was interestitial lung disease (67.8%). No significant difference was found between Y chromosome levels of patients with either lung, cardiac, renal, or gastrointestinal involvement and those who did not have these complications. Y chromosome serum levels based on the results of PFT were also shown to have no significant difference. Moreover, no association was demonstrated between serum Y chromosome and skin score. The serum level of chromosome Y has no impact on the severity and frequency of major organ involvement in Iranian scleroderma patients.