We aimed to determine the prevalence of five intestinal protozoa in cancer and organ transplant recipient patients with molecular methods. This case-control study in a university hospital examined stool samples with microscopy-based conventional and polymerase chain reaction (PCR)-based molecular techniques to determine the existence of five principal protozoa (Cryptosporidium spp., Giardia spp., Entamoeba histolytica, Blastocystis spp. and Dientamoeba spp.) among 57 cancer patients (CP), 33 organ transplant recipient patients (OTP), in comparison with 90 healthy individuals (HI) from Turkey. The overall frequency of intestinal protozoa was 17.2% (31/180) using microscopy and 51.7% (93/180) using PCR. Because of its high sensitivity, PCR was compared with microscopy in terms of the accuracy of detecting intestinal protozoa, and the agreement was found to be inadequate (kappa=0.217; P<0.001). According to the protozoa species, distribution of multiparasitism (68.2%; 22.7%), Cryptosporidium spp. (53.8%; 30.8%) and Giardia spp. (55.6%; 18.5%) were found in CP and OTP, respectively (P<0.001). Depending on the patient groups, multiparasitism (26.3%; 15.2%), Giardia spp. (26.3%; 15.2%) and Cryptosporidium spp. (24.6%; 24.2%) were the most frequent agents in CP and OTP, respectively (P<0.001). In accordance with literature review, this is the first study conducted in Turkey clarifying the prevalence of five intestinal protozoa with PCR techniques among these groups, and tries to ensure a ground for further research. Comprehensive consultation and periodic fecal examinations are recommended especially among patients with cancer undergoing chemotherapy using molecular methods in reference laboratories, oncology and/or transplantation departments of hospitals.