The impact of intestinal parasitic infection in renal transplant recipients requires careful consideration in the developing world. However, there have been very few studies addressing this issue in Iran. This study was conducted to determine the prevalence of intestinal parasitic infections in renal transplant recipients in Iran. Stool specimens from renal transplant recipients and control groups were obtained between June 2006 and January 2007. The samples screened for intestinal parasitic infections using direct smear, formalin-ether sedimentation, Sheather's flotation and modified Ziehl-Neelsen staining methods. Out of 150 renal transplant recipients, 33.3% (50), and out of 225 control group, 20% (45) were infected with one or more type of intestinal parasites. The parasites detected among patients included Entamoeba coli (10.6%), Endolimax nana (8.7%), Giardia lamblia (7.4%), Blastocystis spp. (4.7%), Iodamoeba butschlii (0.7%), Chilomastix mesnili (0.7%) and Ascaris lumbricoides (0.7%). Multiple infections were more common among renal transplant recipients group (p < 0.05). This study highlights the importance of testing for intestinal parasites among Iranian renal transplant recipients. Routine examinations of stool samples for parasites would significantly benefit the renal transplant recipients by contributing to reduce severe infections.