Polycystic ovary syndrome (PCOS) is a hormonal disorder with complex, multifactorial and still not fully explained etiopathogenesis. It is believed that the cause is a combination of genetic and environmental factors. Background: With the aim to better understand PCOS etiology, the study examines body composition and compares the occurrence of lipid disorders and visceral adipose tissue depending on the adopted Rotterdam phenotypes. Methods: The study included 242 patients classified into four classic Rotterdam phenotypes. Clinical data from patients were collected and carefully analyzed to determine the relationship between the occurrence of lipid disorders and the visceral adiposity index (VAI). Results: The results obtained after assessing the differences between the Rotterdam phenotypes were not statistically significant. Differences in the levels of coefficients included in the VAI equation in the given phenotypes were also analyzed, as follows: waist circumference (p-value = 0.3415), BMI (p-value = 0.7112), TG [mmol/L] (p-value = 0.5341) and HDL [mmol/L] (p-value = 0.2302). None of the differences were statistically significant. Conclusions: Although the results did not show a clear association between VAI and the individual Rotterdam PCOS phenotypes, this coefficient can be used in the assessment of cardiometabolic risk in women with PCOS regardless of the adopted classification.