This study was done to assess testosterone deficiency in males with metabolic syndrome (MetS) and the effect of testosterone replacement on insulin resistance and biochemical parameters of this syndrome with hypogonadism. Sixty three males fulfilling the International Diabetes Federation 2005 MetS guidelines as cases and 32 healthy males as controls with the mean age of 35.29±8.16 and 34±6.76 years respectively were enrolled in the study. Fasting blood samples were collected for gonadal profile and insulin assay. Homeostasis model assessment for insulin resistance (HOMA-IR) and free testosterone index were calculated. Hypogonadism was defined when the calculated free testosterone value was <0.225 nmol/L. Total and calculated free testosterone, sex hormone binding globulin (SHBG) were lower in cases than controls (P<0.001). Hypogonadism was seen in 19 (30%) cases with MetS while 1 (3.1%) in controls. MetS cases with hypogonadism had significantly higher HOMA-IR than eugonadal cases. Hypogonadotropic hypogonadism was observed in 16 (84%) cases. Treatment with oral Testosterone 40 mg twice a day for 3 months led to significant improvement of HOMA-IR (P≤0.001) in the MetS males with hypogonadism. This study revealed that males with MetS with or without diabetes had lower serum testosterone than their age matched healthy subjects. Hypogonadism was also common in subjects with MetS. Testosterone therapy to correct hypoandrogenimia improved insulin sensitivity and other biochemical parameters except High density lipoprotein cholesterol in MetS. This emphasizes that hypogonadism in all men with MetS or MetS in all men with hypogonadism needs clinical evaluation and subsequent management.