Backgrounds Many wild-caught reptiles harbor some kind of parasites. Captivity with negative effect of poor sanitary and husbandry management may lead to clinical disease. The increasing trend in keeping non-native reptile species in the last decade emerged a need for the specification of reptile parasites and their hosts. Objectives The study aims to gain data on intestinal parasites of reptiles kept as pets or in small private collections in close contact with people. Methods A combination of native and iodine stained direct smears along with flotation concentration were used to investigate parasites in pet reptiles’ feces. All samples were investigated macroscopically and a smear was prepared and stained by modified Ziehl Neelsen for detection of Cryptosporidium. Results Stool samples from 100 pet or small zoological reptile collections (Lacertilia=36, Serpentes=20, Chelonii=11, Corocodilia=1) were collected. The total occurrence of parasite was 52%. 64.8% of the examined Lacertilia, 35.3% of Serpentes, 45.5% of Chelonii were infected. Eimeria, Isospora, Cryptosporidium, Trichomonas, Balantidium, Strongylid and Oxyurid eggs and amoeba were identified. Cryptosporidium was detected in Lacertilita, Serpentes and Chelonii. In the only sample from a Nile crocodile no parasites were detected. Eimeria was detected in Bearded dragon, Indian python, Albino python and king cobra and Isospora was identified in Bearded dragon and the alien Cheloniid species Red-eared slider. Amoeba was identified in Iguana iguana and Horsfield tortoise. Conclusions Trichomonads, Balantidium, Cryptosporidium, Isospora, Eimeria, amoebae and nematode eggs were identified in the investigated samples. Cryptosporidium were detected by specific stains in 14 samples. Sauria was the most infected suborder (64.8%) while 32.4% of snakes and 45.5% of chelonians were infected. Parasites are common in pet reptiles but the parasite species, the degree of infestation and hygienic management will determine the ultimate clinical outcome of the existing parasite infections. Hence examination for endoparasites should be recommended for checking the health status of all captive or newly entering reptiles.