Scleroderma is a rarely seen chronic collagen tissue disease which has been first described in the 18th century. It is indicated that the mutations in BMPR2 (bone morphogenetic protein receptor type II) gene affected the course of disease.In this study; determination of BMPR2 gene expression levels via Real Time PCR and its association with the clinical course in scleroderma patients were revealed.20 Scleroderma diagnosed and 29 healthy individuals were taken into this study. Performing the transformation of cDNA complementary to mRNA isolated from leucocyte cells, DNA amplification was carried out via Real-Time PCR. To determine the relative expression level of BMPR2 gene via Real-Time PCR, Beta actin gene was selected as the reference gene.Mean expression levels of BMPR2 gene in patient group showed significant decrease in comparison with control group (Cp<0,05). Expression levels of patients decreased around 39,46% in comparison with control group. 4 of these 20 patients included into the study diagnosed with PAH (Pulmonary Arterial Hypertension) and gene expression levels of these patients were seen to increase.Normalized data was analyzed by using mixed model and statistically different groups were determined by Minimal Important Difference (MID) test.Consequently, in Scleroderma patients BMPR2 gene expression level showed changes from person to person but it decreased by comparison to healthy control group and in patients withPAH that was foundto be higher than the gene expression levels of other patient group