Purpose There is a relationship between polycystic ovary syndrome (PCOS) and adipose tissue dysfunction (ADD), but this relationship is not clear. It has been recently shown that iron accumulation in adipose tissue is among the causes of adipose tissue dysfunction. Data on adipose tissue dysfunction in women with PCOS are insufficient. In this study, we aimed to evaluate the relationship between serum ferritin levels (iron accumulation biomarker) and visceral adiposity index (an indicator of adipose tissue dysfunction). Methods The study is a case-control study. Women with diagnosed PCOS with 2003 Rotterdam Diagnostic Criteria (n = 40) were compared with non-PCOS group (n = 40). In this study, the cholesterol ratios, the homeostatic model evaluation index for insulin resistance (HOMA-IR) and the quantitative insulin sensitivity control index were calculated using biochemical parameters, and the visceral adiposity index (VAI) and the lipid accumulation product (LAP) were calculated using both anthropometric and biochemical parameters. In this study, insulin resistance was evaluated by HOMA-IR and adipose tissue dysfunction was evaluated by VAI index. Results According to the results of this study, women with PCOS have a worse metabolic status than women without PCOS. However, this has been shown only in overweight and obese women, not in women with normal weight. Conclusion As a result, the presence of obesity in women with PCOS exacerbates metabolic status.