Chronic obesity can lead to inflammation of the testes which can affect the production of testosterone and spermatogenesis. As omega 3 is acting as an anti inflammatory, this study aimed to investigate the effects of omega 3 on serum testosterone levels and quality of spermatozoa in obese rats. 25 male rats, 2-3 months old and weighting 160-240 g were divided into 5 groups. The control group was given a standamrd diet. The treatment 1 group received high fat diet and cheese while the treatment 2, 3, and 4 groups were given high fat diet and cheese for 6 weeks followed by omega 3 administration at doses of 28.8, 46.8, and 64.8 mg, respectively during the next 51 days . At the end of treatment period, serum testosterone levels were analyzed by ELISA, and sperm amount, motility, viability, and morphology were observed under a digital microscope. Data were analyzed using one way Anova test followed by Bonferroni post hoc test to analyze the differences of influence between groups. Results showed that serum testosterone levels as well as the amount and viability of spermatozoa were not significantly different between studied groups (P= 0.230, P= 0.071, and P= 0.241, respectively). The mobility of spermatozoa (P= 0.039), and their morphology (P= 0.047) were significantly affected by omega 3 treatment. Omega 3 may affect fertility by improving the motility and morphology of spermatozoa.