Polycystic ovary syndrome (PCOS) is the most common endocrine-metabolic disorder in women of reproductive age. Most PCOS patients have a tendency to become obese and insulin resistant. Omentin-1 is an anti-inflammatory adipokine and plays a role in regulating insulin sensitivity. Apelin is a new adipokine which may be a key regulator in glucose and lipid metabolism and may be associated with insulin resistance. This study aimed to evaluate serum levels of Omentin-1 and Apelin to determine their association with obesity and IR in PCOS. A total of eighty subjects divided into four groups: Group I: 20 non-obese control (BMI< 30), Group II: 20 non-obese patient with PCOS (BMI< 30), Group III: 20 obese Control (BMI ≥ 30) and Group IV: 20 obese patient with PCOS (BMI ≥ 30). Serum levels of Insulin, Omentin-1 and Apelin were estimated by ELISA. Homeostasis Model of Assessment-Insulin Resistance (HOMA-IR) was calculated. Results showed a significant decrease in serum levels of Omentin-1 and increase in serum levels of Apelinin (non-obese and obese) PCOS groups when compared to their controls. Within PCOS groups there were significant negative correlations between Omentin-1 and both of HOMA-IR and BMI, while there were significant positive correlations between Apelin and both of BMI and HOMA-IR. In summary serum Omentin-1 and Apelin are directly correlated with IR and obesity in women with PCOS.