Diarrheal diseases cause significant morbidity in developing countries, and have a potential to cause severe complications. Stool samples collected from 272 patients with diarrhea in Adana, Turkey were screened using different laboratory methods such as the wet mount examination (WME), modified trichrome stain (MTS), modified acid-fast (MAF) stain, enzyme linked immunosorbent assay (ELISA) and real-time polymerase chain reaction (real-time PCR) for intestinal parasites. Intestinal parasites were detected in 25.4% (69/272) of the patients. Of the parasites detected, Cryptosporidium spp. was the commonest 10.3% (28/272) followed by Blastocystis spp., 5.9% (16/272), Entamoeba dispar 2.6% (7/272), Giardia lamblia 2.6% (7/272), Entamoeba coli 1.8% (5/272), Entamoeba histolytica 0.7% (2/272), Isospora belli 0.7% (2/272), Trichuris trichiura 0.4% (1/272) and Strongyloides stercoralis 0.4% (1/272). Our study shows that there are differences in results obtained using different laboratory methods; 22.1% (60/272) with real time-PCR, 10.3% (28/272) with ELISA, 9.9% (27/272) with MTS, 6.6% (18/272) with WME, and 5.9% (16/272) with MAF stain. The differences in the level of positivity using different laboratory methods were sequenced in the diagnosis of intestinal parasites ranging from highest to lowest, as real-time PCR>ELISA>MTS> WME>MAF stain. Molecular techniques are recommended as diagnosis of choice especially in patients suffering from chronic diarrhea.