The aim of this study is to assess the FNDC5 and myonectin expressions and serum levels of myonectin and irisin in women with PCOS. 90 participants were included in this case-control study. 45 of these participants were with PCOS, and 45 of them were healthy volunteers matched for age and body mass index (BMI). Serum irisin and myonectin levels were measured with commercially available enzyme-linked immune sorbent assay (ELISA) kits. Expression of the myonectin and FNDC5 genes were determined by RT-PCR analysis. It was found out that FSI, HOMA-IR, LH, LH/FSH, TT, serum irisin and serum myonectin levels, myonectin mRNA expression, and FNDC5 mRNA expression were higher in the PCOS group, whereas HDL-C level was lower in the PCOS group (p < .05). When the groups were compared, it was detected that IR and HA were significantly higher in the PCOS group (p < .05). Serum irisin and myonectin levels, and myonectin and FNDC5 mRNA expressions were increased in women with PCOS. These molecules can be target molecules in PCOS pathophysiology and treatment.IMPACT STATEMENT What is already known on this subject? Although the aetiology of PCOS is not fully understood, it is thought that insulin resistance may play a critical role. In recent studies, the relationship of cytokines secreted from skeletal muscle with insulin resistance has been shown. The effects of irisin and myonectin, which are members of the myokine family, on lipid and glucose metabolism are known. What do the results of this study add? Although there are many studies in the literature regarding serum irisin levels in women with PCOS, their results are confusing. There is a study in the literature investigating the relationship between myonectin and PCOS. In our study, we evaluated myonectin and FNDC mRNA expressions in addition to serum irisin and myonectin levels. As a result, we found that markers and their mRNA expressions were lower in patients with PCOS compared to controls. What are the implications of these findings for clinical practice and/or further research? We think that the results of our study will shed light on future studies. Due to their effects on adipose tissue, these markers may play a role in the aetiology of long-term complications of PCOS. Moreover, they can become pharmacological targets in preventing these complications.