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Background: Opportunistic microorganisms of the intestinal tract, such as Cryptosporidium spp. Giardia spp. Blastocystis sp. and microsporidia, are increasingly responsible for clinical disorders in various host species, including humans. Objectives: This study was conducted to search for the above parasites in the feces of pet birds using parasitological and molecular methods in Tehran City, Iran. Methods: In the current study, fecal samples of avian birds were collected and investigated with modified Ziehl-Neelsen, modified trichrome, and trichrome staining for the presence of microsporidia, Cryptosporidium, Blastocystis and Giardia. All the samples were examined molecularly with specific primers and PCR methods. Results: Three of the examined droppings contained Encephalitozoon hellem genotype 1B (2%) by PCR and sequencing. The microsporidian organisms were recovered from the droppings of a clinically normal green-cheek parakeet, an African gray parrot, and a lovebird. Other parasites that were examined were not found in the analyzed samples. Conclusion: The current study proved that captive pet birds are a possible source of microsporidian infection. Besides the fact that encephalitozoonosis is predominantly subclinical in birds, the highly resistant nature of the microsporidia spores can put the owners at increased risk of disease acquisition via spore inhalation or ingestion. [ABSTRACT FROM AUTHOR]