Polycystic Ovary Syndrome (PCOS) is a common reproductive health problem associated with long term complications. It is a condition of high clinical heterogeneity with familial clustering, however, the mode of inheritance is still controversial. A number of candidate genes have been implicated in susceptibility to PCOS, suggesting a strong role of genetic factor in the aetiopathogenesis of PCOS. The aim of the present study was to determine possible association between PCOS and family history of complex genetic diseases such as PCOS, Menstrual disturbance, type II Diabetes and Cardiovascular diseases. A total of 432 individuals comprising of 206 patients and 226 controls were involved in the present study. Clinical information, anthropometric measurements and three generation pedigree data with respect to CD was collected through proforma. Twenty five percent of PCOS probands exhibited clinical hyperandrogenism in the form of hirsutism, acne, premature pubarche and alopecia. Eighteen percent showed acanthosis, a marker for insulin resistance. Twenty percent of the patients were under the category of amenorrhea; while remaining 75% of cases were either with primary/secondary infertility. The anthropometric analysis revealed higher BMI and W/H ratio in the patient group compared to the controls. A high frequency of PCOS women exhibited the prevalence of complex diseases in their families compared to the control families (60 vs. 20%; p<0.05). It is suggested that complex diseases provide significant genetic background for the susceptibility to develop this multifactorial disorder in a section of patients.