Kidney transplant recipients routinely use immuno­suppressives and are susceptible to a variety of infections. Data on the prevalence of parasitic and fungal bowel contaminations in Iranian transplant recipients are limited. This study was conducted to address the issue in a controlled cross-sectional study. A total of 150 kidney transplant recipients and 225 outpatient controls referred to the central laboratory of transplantation were enrolled. Stool sample was obtained from all participants and direct examination, concentration, color-blending and cultures were performed using standard methods. The prevalence of bowel contamination with parasites and fungi in transplant recipients were 33.3% and 58.7%, and in healthy controls were 20.0% and 51.1%, respectively (p>0.05). Entamoeba Coli was the most common parasitic contamination with an estimated prevalence of 9.3% in transplant and 6.7% in control groups. Candida species were the most prevalent fungal contaminations and were found in 22.0% of transplant patients and 24.4% of healthy controls. Co-infection with two or more fungi was observed in 14.8% of transplant patients and 3.4% of controls (p<0.001). In conclusion, although the prevalence of parasitic and fungal contaminations were comparable in two groups, high contamination rate especially co-infection with multiple fungi in transplant recipients warrants for pretreatment evaluation of these patients. However, the pathogenicity of these contaminations needs further assessments.