Eighteen NZW rabbits used for local skin irritation study were examined grossly and microscopically for natural infection with Encephalitozoon cuniculi. For microscopic tissue evaluation histochemical techniques such as PAS Gram iron hematoxylin and HE stain were used. Although rabbits in the study had no abnormal clinical signs 7/18(38.9%) animals were microscopically infected with E. cuniculi. The affected rabbits had gray-whitish and depressed approximately 0.1∼0.6 cm diameter lesions in the kidneys. All other organs examined were grossly unremarkable. Histopathologically however in addition to segmental interstitial nephritis focal lymphocytic myocarditis and granulomatous inflammatory reaction in portal areas of the liver multifocal granulomatous foci with vasculitis were present in the brain kidney and lungs. Aggregates of minute oval organisms were observed in brain and kidney sections frequently within the granulomatous foci and sometimes without any inflammatory reaction particularly in the renal tubules. in histochemical stains the organisms were gram positive stained with iron hematoxylin and had PAS positive granule at one pole. They measured approximately 1.5×2.5μm consistent with E. cuniculi. Histochemical characterization is important to differentiate E. cuniculi from other common protozoal infection such as Toxoplasma gondii. This study demonstrate the importance of subclinical. E. cunuculi infection and the associated histological alterations may interfere with tissue evaluation in toxicologic studies