Aspergillus flavus is considered a one of the fungi which can cause dangerous fungal infections for humans and animals. In this study, an isolate of this fungus was  identified according to the morphological and molecular methods. The polymerase chain reaction ( PCR )  was used to confirm the identification of the isolate appeared genes of the A. flavus ( FLA ) and a putative RNA-Pol II transcription elongation factor ( RtfA) which located in 497  and 263 base pairs ( bp), respectively. Experimentally, two groups of the albino male rats were used in this study  by which one group was immunosuppressed and infected with 0.5 ml containing 10 ⁶ spores of A. flavus intra-peritoneally  while other group was inoculated with 0.5 ml of the sterile normal saline. Brains of the infected rats revealed lesions that the brain appeared swelling and congestion of the cerebrum pushing the cerebellum down. Cerebral cortex with prominent haemorrhagewas illustrated with lymphocytic infiltration. Also, demonstrating pyogenic granuloma in the cerebral cortex composed of centre of caseous necrosis surrounded by massive neutrophils and other chronic inflammatory cells. In addition, the brain sections possessed multiple multinucleated giant cells and dissemination of A. flavus into ventricular space and choroid plexus.