BACKGROUND Childhood cancer treatment negatively affects the immune system, increasing the risk for bacteremia and septicemia. As the oral cavity is a major entry portal for pathogens into the bloodstream dental care in such children tends to be radical, favouring tooth extraction over less drastic treatments such as pulpotomy, the amputation of infected dental pulp. The present study aimed to compare pulpotomy treatment success rate in children with cancer receiving immunosuppressive therapy with that of healthy children, and investigate if unsuccessful pulpotomy treatment in oncologic patients may lead to systemic complications. METHODS Twenty-six medical records of children from a paediatric oncology referral centre who had dental pulpotomy treatment (in 41 teeth) while receiving active cancer care during the years 2006-2012 were compared with records of 41 randomly selected healthy children who had undergone pulpotomy treatment (41 teeth) in the same institute during these years. Clinical and radiographic data were collected during treatments and at the end of the follow-up period (six months post dental treatment). RESULTS No statisticaly significant difference was found between pulpotomy success rate amongst the two groups. Treatments success rates in the study and control groups were 82.9% (± 5.9) and 90.2% (± 4.7), respectively. No patient in the study group suffered from sepsis from a dental origin during follow-up period. CONCLUSIONS Pulpotomy in paediatric cancer patients did not increase the risk for bacteremia or systemic complications from oral origin. We therefore recommend the re-evaluation of the current protocol for treating paediatric oncology patients.