OBJECTIVES:  Exposition to microwave radiation (MW), from mobile phones, satellite communications, radio relays, radars and microwave devices in medicine induce disturbances in thymus. The pineal secretory product, melatonin (Mel), exerts a veriety of effects on the immune system. The aim of the present study was to evaluate the effect of melatonin on apoptosis and oxidative stress parametars in thymus tissue of rats after 40 days long exposure to MWs. METHODS:  Wister rats were divided in 4 experimental groups: I (control), II (Mel group) - rats treated with Mel every day (2 mg/kg b.w., i.p), III (MW group) - rats exposed to MW (4 h/day), IV (MW+Mel) - rats treated with Mel every day (2 mg/kg b.w., i.p) and exposed to MW radiation (4 h/day). Ten animals from 4 group were successively sacrificed after 40 days of the experiment. MW was produced by a mobile test phone (SAR = 0.043-0.135 W/kg). RESULTS:  The current study results demonstrate that MW significantly increased thymocyte apoptosis, detected using the Annexin V-FITC/PI detection kit (p<0.001). DNA fragmentation in thymocytes injury of MW is probably triggered by the increase activation of alkaline-DNase I (caspase 3-activated) and acid-DNase II (p<0.05). A significant increase in the thymus malondialdehyde (MDA) and carbonyl group concentration (p<0.001), and decreased activity of catalase (p<0.001) was registered during exposure. Melatonin was found to be effective on rat thymocyte: (1) decreased apoptotic rate of thymocytes (p<0.001), (2) effect on terminal apoptotic reaction, because of the decrease DNase I and DNase II activity (p<0.01), (3) decreased MDA and carbonyl group levels (p<0.01), (4) increase activity of catalase (p<0.05), comparated with MW group. CONCLUSIONS:  Having in the mind obtained results we can conclude that melatonine exerts protective effects on rat thymocyte by preventing apoptosis and oxidative stress disturbances in rats' thymus under exposure of MW.