Objective: To investigate the intestinal protozoans using different diagnostic methods among 558 patients with gastrointestinal symptoms and to evaluate the contributions of these methods to the diagnosis. Material and Methods: Native-lugol, trichrome and Kinyoun's Acid Fast (KAF) stain methods were used for microscopic examination of fecal samples of 558 patients. Entamoeba histolytica, Giardia intestinalis and Cryptosporidium parvum were examined by ELISA in fecal samples, while Direct Florescent Antibody (DFA) (CRYPTO/GIARDIA CEL, Cellabs, Australia) tests were also used for both G. intestinalis and C parvum concurrently. Real-time polymerase chain reaction (PCR) was employed to study the DNA of E. histolytica in fecal samples from 90 patients with diarrhea containing mucus and blood who were suspected to have amebiasis. Results: The examination of 558 patients revealed that the most common protozoan was Blastocystis hominis (10% with native-lugol, 11.8% with trichrome stain). Five different protozoans were detected with native-lugol while the number increased up to seven when trichrome stain method was used. The sensitivity, specificity, and reliability [kappa (kappa) values] of the microscopic methods used for the diagnosis of G. intestinalis, E. histolytica, and C parvum compared with immunodiagnostic methods varied between 26.0-75.0%, 97.6-100.0%, and 0.20-0.66 (low or medium level) respectively. When real-time PCR was used, E. histolytica DNA tested positive for two (2.2%) of the four samples which were positive with ELISA. Conclusion: ELISA, DFA and real-time PCR are very practical and useful methods for the identification of intestinal protozoan infections in routine laboratories.