Polycystic ovary syndrome (PCOS) is a complex hormonal disorder in reproductive-aged women. Various features of this disorder have an influence on bone metabolism giving it an unusual protective mechanism for bone health as compared to non PCOS females. The current treatment of PCOS however nullifies this bone protective effect resulting in low Bone Mass Density (BMD) in patients under treatment. As described earlier PCOS women as a result in hormone imbalance due to the disease have higher Bone Mass Density as compared to healthy females of same age group. While getting treatment for PCOS to improve fertility in these patients this protective mechanism is lost. Currently no established treatment option is available which can increase the fertility of these patients while preserving the BMD advantage. Many studies have suggested that by maintain optimum androgen – estrogen ratio in patients with PCOS, BMD and fertility both can be balanced out. No such data is available for local Pakistani population although this is amongst the most commonly occurring hormonal disorder occurring in our female population. Developing an algorithm of the results is to help early diagnosis and prevention of these disabling diseases. This criterion can be used in e-medicine and treatment plan can be established using the application after the values of the result are entered as well as be used to modify existing drugs to preserve the benefits of PCOS while increasing the fertility of the patients in collaboration with pharma industry.