Polycystic ovary syndrome (PCOS) is the most common, yet complex, endocrine disorder affecting women in their reproductive years. The etiology of PCOS is still unknown, yet, there is increasing evidence to support a major genetic basis, as the syndrome have strong familial predisposition. More than one gene were contributes to the heterogeneous phenotype and the clinical and biochemical presentation. Patients with PCOS may present complaining of irregular or unpredictable menstrual cycles, unwanted hair growth, acne or scalp hair loss, or unexplained weight gain or overweight, infertility. Clinical phenotyping of PCOS involves determining the presence of clinical and/or biochemical androgen excess. The bulk of evidence points to theovary being the source of excess androgens, which appears to result from an abnormal regulation of steroidogenesis. The androstenedione is converted to estrogens by the action of aromatase enzyme which was encoded by cytochrome p450, family19 (CYP19) located on the long arm of chromosome 15. Several single nucleotide polymorphisms of the CYP19 gene were associated with variation in serum androgen concentrations among women; one of it is the SNP rs2414096. Most women with PCOS (obese or non-obese) suffer from insulin resistance. The cellular and molecular mechanisms of insulin resistance in PCOS is a decrease in insulin sensitivity secondary to a post binding abnormality in insulin receptor-mediated signal transduction, with decrease in insulin responsiveness, this appears to be potentially an intrinsic defect in genetically susceptible women. The insulin receptor is encoded by the INSR gene which is located at the chromosome 19. Several kinds of polymorphisms have been identified within INSR. Of these polymorphisms, most were single nucleotide polymorphism of the C/T SNP at His1058 in exon 17 of INSR. This work was conducted to study: 1. The effect of(CYP19) genes polymorphism in PCOS hyperandrogenemia. 2. The role of insulin receptor gene (INSR) in glucose tolerance and lipid metabolism in obese and non-obese PCOS women. Eighty-four infertile Iraqi women with PCOS fulfilling at least two of the three Rotterdam criteria. Sixty-five women free from signs and symptoms of PCOS were studied as control group. Both groups were subdivided in to two subgroups obese (BMI ≥30 kg/m2) and non-obese (BMI <30 kg/m2). All PCOS patients and control women subjected to the measurement of: 1. BMI, waist/hip, waist/thigh ratio, ultrasound examin in cycle day 12-13. 2. Hormonal examination of FSH, LH, E2 and testosterone in cycle day2-3. 3. Biochemical tests include glucose tolerance test. 4. Lipid profile test (cholesterol, triglyceride, LDL, VLDL and HDL). 5. Molecular analysis: In this research we analyze the single nucleotide polymorphism of INSR &CYP19 genes by using restriction fragment length polymorphism (RFLP) analysis. There were significant higher BMI, waist/hip, waist/thigh ratio in PCOS patients compared to control women even between the subgroups. There were significant lower FSH, higher LH, E2 and testosterone, lower E2/testosterone ratio in PCOS patients compared to control women, while no significant difference between obese and non-obese PCOS, obese and non-obese control women. Significant higher level of blood sugar (fasting, after 1/2, one and two hours) observed in PCOS compared to control group regardless of their weight. The PCOS patients have significant higher level of cholesterol, triglyceride, VLDL, LDL and lower HDL than control women. Similar results observed between obese PCOS and obese control, obese and non-obese PCOS, while it was higher but not significant between non-obese PCOS and non-obese control, and between obese and non-obese control women. Regarding the genotypic distribution of INSR gene, there was significant difference between PCOS patients and control women, and between obese (PCOS vs control), whereas no significant difference between non-obese (PCOS vs control), PCOS (obese vs non-obese) and between control (obese vs nonobese). With regard to the CYP19 gene there was significant difference between PCOS and control and between obese (PCOS vs control), while no significant difference between non-obese (PCOS vs control), PCOS (obese vs non-obese) and between control (obese vs non-obese). Concerning the allelic frequency of INSR gene, the study showed higher frequency of C and low frequency of T alleles but not with CT between PCOS vs control. Also there was higher frequency of C allele and lower but insignificant T allele between obese (PCOS vs control). Similar results were demonstrated between non-obese (PCOS vs control). No significant difference in the allelic frequency distribution between PCOS (obese vs non-obese) and between control (obese vs non-obese). The allelic frequency of CYP19 gene showed significant lower frequency of A allele and non significant higher AG and G allele in PCOS compared to control women. Between the obese (PCOS vs control), there was significant lower frequency of A allele and higher frequency of G allele but not with AG allele. No significant difference in the allelic distribution between non-obese (PCOS vs control) and between PCOS (obese vs non-obese) and also between control women (obese vs non-obese). PCOS patients who have C allele of INSR gene showed significant higher BMI and waist/hip ratio than those with CT and T alleles but not in the control women. PCOS patients and control women with C allele have significant higher blood glucose (FBS, blood sugar after half, one and two hours), higher cholesterol, triglyceride, LDL, VLDL and lower HDL than those with CT and T allele. PCOS patients and control women with A allele group of CYP19 gene have significant higher E2, lower FSH, LH, testosterone level and E2/testosterone ratio than those with AG and G allele. It is concluded from this study that a single nucleotide polymorphism in the tyrosine kinase domain of the INSR gene was associated with PCOS and its obese & non-obese subgroups, also with insulin resistance and atherogenic lipoprotein which has role in the pathogenesis of PCOS. Also the findings of the present study support the hypothesis CYP19 gene variants play a synergistic role in the hyperandrogeni phenotype of PCOS, since it was associated with PCOS and hyperandrogenism