Background: Tropheryma whipplei is the causative pathogen of Whipple’s disease and other acute and chronic manifestations. Children have been identified as reservoirs of this bacterium especially in low-middle income countries. No information is currently available on the dissemination of T. whipplei in Iran. Therefore, the aim of this study was to investigate the presence of T. whipplei in children with immunodeficiency. Methods: This cross-sectional study was performed from July 2018 to February 2019 in Qom province (central Iran). Stool samples were collected from immuno-compromised children. T. whipplei was tested by SYBR Green and Taq-Man Real-time PCR assays. For confirmation, sequencing of the isolated bacteria was done. Results: One hundred and 30 children with a mean age of 56.7 months were enrolled. Acute lymphocytic leukemia was the most reported immunodeficient disease (77%), followed by non-Hodgkin lymphoma and retinoblastoma. The majority of the children were undergoing chemotherapy during the study. Thirteen (10%) children had T. whipplei DNA in the collected stools. Sequencing results confirmed T. whipplei identification in all the cases. Eight out of 70 (11.4%) children under 5 years old resulted positive. Conclusion: This is the first study showing the circulation of T. whipplei among immunocompromised children in Iran. More epidemiological studies are needed to evaluate the prevalence of this pathogen in different risk groups in Iran and to increase the knowledge of its rare clinical manifestations.