This study included 120 of obese males with mean age 20-50 year and 50 aged-matched healthy males as a control. The obese patients classified into 3 groups based on Body Mass Index (BMI). DNA was isolated from the collected blood samples and applied for PCR using primers designed for exons 3 and 9 of FTO gene. The results showed that there are 8 mutations in the exon 3. Seven of the mutations are transition and one is transversion. Furthermore, seven of which are predicted to be missense and one is silent. As for exon 9, twelve mutations were identified. Eight of the mutations are transversion and 4 are transition, whereas eleven of which are predicted to be missense and one is silent. The mutations in both 3 and 9 exons recorded a significant differences (p ≤ 0.05) with a Chi-square (X2) 63.229 and 24.802 respectively in the incidence of the pathogenicity comparison to the control.