Our objective was to investigate alterations in the developing mice brain after intrauterine microwave exposure from different gestation days (0.25 and 11.25) till term. Pregnant mice from 0.25 and 11.25 days of gestation were isolated from an inbred colony and divided into sham-exposed (control) and microwave-exposed (10 GHz) groups. The follow-up study of mice at 3 weeks of age showed significant reduction in the brain and body weight of microwave-exposed group. Results showed an increased level of lipid peroxidation, decreased level of glutathione and protein after microwave exposure on both 0.25 and 11.25 day of gestation. Moreover, changes in cytoarchitechure of hippocampus and cerebellum of the brain and reduction in Purkinje cell number were observed statistically significant after microwave exposure from both 0.25 and 11.25 days of gestation. In conclusion, the degree of severity of damage in neonatal mice brain was much higher, when exposure started from 0.25 day of gestation compared to 11.25 days of gestation.