Introduction: We aimed to determine the frequency and microbiological causes of diarrhea occurring during the first 100 days in allogeneic (allo-) and autologous (auto-) stem cell transplantation (SCT) patients. Methodology: A total of 452 patients who underwent transplantation due to hematological or solid organ malignancy were included. From the administration of the conditioning regimen up to day 100 post-transplant, diarrhea cases lasting at least three days with a minimum of three episodes per day were evaluated. Results: Cases of diarrhea were observed in 94 patients out of 227 subjects who received allo-SCT and in 107 patients out of 225 who received auto-SCT. The incidence rate of diarrhea in both patients undergoing autologous and allogeneic transplant was 47.5% and 41.4%, respectively. The cause of the diarrhea could be detected in 20.5% of auto-SCT patients and in 30.8% of allo-SCT patients. Parasitic infections were frequently observed in both autologous and allogeneic transplant patients in the first 20 days. In the late period, significantly more patients developed diarrhea in the allo-SCT recipient group than in the auto-SCT recipients due to graft versus host disease (GVHD) and cytomegalovirus (CMV) colitis. Conclusions: This study revealed the causes of diarrhea and the prevalence and factors of parasitic infections in transplant patients in Turkey. All causative factors of diarrhea should be considered in detail, feces analyses should be evaluated for each patient, and endoscopic biopsy samples should be obtained when required in immunosuppressive patients undergoing stem cell transplantation. © 2014 Pala et al.