Objectives: To evaluate possible associations between the genetic polymorphism of the STK 11 gene and response to metformin in women with polycystic ovary syndrome. Methods: This is a prospective longitudinal cohort study of 57 women with polycystic ovary syndrome. Baseline documentation of anthropometric measurements, menstrual history, hirsutism, hair loss, acne, and biochemical parameters, in addition to gene testing for STK11 polymorphism, were performed. Follow-up was arranged at 6 cycles following oral metformin therapy, 850 mg, twice daily. Results: Post-metformin therapy, there were statistically significant improvements in menstrual frequency, blood loss, acne, ultrasound findings, and a decrease in BMI, acne and hirsutism, but not in alopecia. Fasting insulin decreased significantly, but fasting blood sugar did not. Regarding Intron1 polymorphism, there was a significant response in the CC subgroup in menstrual regularity and blood loss. The CG subgroup showed a significant response in menstrual regularity and ultrasound findings. The GG subgroup showed a significant response in menstrual regularity, menstrual loss, acne and alopecia. Regarding Intron 6 polymorphism, there was a significant response in the CC subgroup in relation to menstrual regularity, blood loss, acne and ultrasound findings. The CT subgroup showed a significant response in menstrual regularity and ultrasound findings. The TT subgroup showed a significant response only in relation to alopecia. Conclusion: Polymorphism in STK11 is not predictive of response to metformin therapy at a dose of 850 mg, twice daily.