Introduction: There is not much data on parasitic infections of laboratory animals that are kept in conventional conditions in Iran. The present study was designed to investigate intestinal helminths infections in laboratory colonies of rats and mice. Methods: Droppings from 110 mice and 110 rats (each animal one dropping) belonging to experimental and breeding groups in four animal houses were collected. Experimental groups were being used in biomedical researches and breeding groups were not under any experiment. The droppings were preserved in formaldehyde 10% individually and examined by microscopy with 10x magnification. Results: Out of 220 droppings examined, 96 (43.6%) harbored helminths eggs; 53 (48.1%) belonged to mice and 43 (39.09%) to rats. Four helminthes species including, Syphacia obvelata, Syphasia muris, Hymenolepis nana, and Hetrakis spumosa were identified in the both animals, while Aspicularis tetraptera was merely seen in mice. H. nana was the most frequent helminth infection in mice and rats and infection with H. spumosa and A. tetraptera, showed the lowest rates in droppings of mice and rats, respectively. Mixed infections with ≥ two species was observed in 21 (9.5%) of 220 droppings, 14 (12.7%) belonged to mice and 7 (6.3%) to rats. Conclusion: The present results emphasizes more careful monitoring in laboratory animal houses, such as improving the cleaning and ventilating systems as well as adopting therapeutic measures, when required.