Polycystic Ovarian Syndrome (PCOS) has now become more common in occurrence in women of reproductive age, particularly in urban and semi-urban population in India. So there is a need to investigate this phenomenon taking into consideration various aspects including possible treatment method to ameliorate/eradicate this syndrome, which has far reaching socio-economic impact and consequences, in view of infertility and irregular menstrual cycles frequently associated with this syndrome. Homeopathy is a branch of traditional alternative medicine which is gaining popularity in India and some other developing countries, as also in some of the developed countries in Europe. With this background scenario, we have made an attempt to treat cases of confirmed PCOS and tried to compare the relative efficacy of two potentized homeopathic drugs, namely, Lycopodium clavatum (Lyco) and Calcarea carbonica (Calc), most frequently used by homeopathic practitioners, selecting different potencies of the drugs, depending on condition/guiding symptom(s) of the patients. While the main focus was pointed on total/partial removal of cysts, data pertaining to different PCOS associated symptoms were also compared for the sake of learning if the two drugs had differential effects on these symptoms also. The study parameters in this investigation included: regularity/irregularity of menstrual cycle, presence/absence of acne, hirsutism, male type alopecia, acanthosis nigricans, body/mass index (BMI) and waist-hip ratio. Overall results provided clear evidences that both these homeopathic drugs had great ameliorating effects on PCOS, although each drug had a little different effect in respect of the individual parameters of this study.