INTRODUCTION: Systemic sclerosis (SSc) is a chronic autoimmune disease of the connective tissue of the unknown etiology. Microchimerism is the presence of a small amount of foreign cells or DNA within the tissue or circulation of an individual. There are two basic types of microchimerism, maternal microchimerism (MMc) and fetal microchimerism, which develop as a result of bidirectional cell turnover in pregnancy. OBJECTIVE: The aim of this study is to investigate the quantitative proportions of Y specific gene regions in DNA samples isolated from periheral leukocytes from both SSc subjects and healthy subjects, and to compare the measured concentrations of Y DNA with the biochemical and demographic characteristics of the subjects. MATERIALS AND METHODS: The study inclued 18 SSc subjects and 10 healthy controls, adult women who gave birth to at least one male child and two positive controls for the male gender. LymphoprepTM medium was used to isolate total peripheral leukocytes (PBMC) from the blood. DNA isolation was performed using the Qiagen QIAamp Mini commercial kit. The DNA concentration was measured by the qPCR method on the QuantStudio 5 using QuantifilerTM Y Human Male DNA Quantification commercial kit. The analysis of STR marker was done on an ABI Prism 310 Genetic Analyzer. RESULTS: The presence and concentraction of Y DNA in the samples of healthy controls and SSc subjects were not recorded. The Y DNA concentraction was successfully analyzed in standard samples and in two positive controls and obtained Y STR profiles of male control subjects. CONCLUSION: The absence of positive DNA in PBMC samples of SSc subjects is a possible consequence of the extremely small amount of Y DNA in the analyzed samples. To confirm the results of quantitative analysis of microchimerism in SSc requires analysis of a larger amount of DNA in higher number of subjects with the selection of more specific gene regions.