The association of anti-infective, antineoplastic and immunosuppressant drugs makes patients undergoing hematopoietic stem cell transplantation susceptible to the effects resulting from drug interactions. In this study, we analyzed the potential drug interactions in the association between anti-infective, antineoplastic and immunomodulators agents and their clinical effects presented by patients from a bone marrow transplant service of a Brazilian hospital specialized in cancer treatment. The retrospective cohort involved patients in the conditioning phase undergoing transplantation in the year 2013. The chi-square test was used to assess the association and the confidence interval considered was 95%. A total of 53 patients were included in the study and 69.8% ( p = 0.004) presented some potential drug interaction. Of these, 97.3% ( p < 0.001) exhibited some symptom that may be associated with these interactions. Interactions with cyclophosphamide and cyclosporine were the most serious effects. There has been a high frequency and variety of interactions that may impair the entire transplant process, putting the patient's life at risk. The potential interactions observed during the conditioning period were associated with the symptoms presented by the patients. Strategies are needed to minimize negative outcomes in transplant patients.