We investigated the prevalence of intestinal protozoan parasites in patients with gastrointestinal complaints in medical centers in Zahedan, Iran. A total of 1562 stool samples was examined from July 2004 to January 2006 using microscopy (direct smear, formalin-ether concentration), xenic culture and PCR techniques. Four hundred and twenty-seven (27.3%) of the patients were infected with one or more intestinal parasites. Giardia lamblia (10.1%), Entamoeba coli (10%), E. hartmanni (1.7%), Blastocystis hominis (2.2%), Chilomastix mesnili (1.7%), Trichomonas hominis (0.7%), E. histolytica/E. dispar (0.51%) and Iodamoeba butschlii (0.45%) were the most prevalent protozoa detected with microscopy. Of the eight microscopy-positive E. histolytica/E. dispar samples, six were identified as E. dispar by PCR/gel electrophoresis, whereas E. histolytica was not detected at all. Although Zahedan is an area with poor hygiene located in a tropical area near the border of Pakistan and Afghanistan, the prevalence of E. histolytica and E. dispar here compared with other parasites and infectious diseases is unexpectedly low.