The objective of this study was to investigate changes in the oral health of children undergoing allogeneic bone marrow transplantation. The study group comprised 23 children undergoing allogeneic bone marrow transplantation and their matched controls. The study group comprised 23 children undergoing allogeneic bone marrow transplantation and their matched controls. Measurements were taken of the mean decayed, missing and filled surfaces and the mean decayed, missing and filled teeth in both deciduous and permanent dentition at baseline, the mean bacterial plaque and gingival inflammation indices and mucositis at specific event-related times during the transplantation period, were measured. The number of decayed, missing and filled surfaces in deciduous teeth was significantly greater in the transplant children than the matched controls (P < 0.05) at baseline. There was a significant increase in both the mean bacterial plaque score for the deciduous teeth (P < 0.003) and the permanent teeth (P < 0.001) and the mean gingival inflammation score for the deciduous (P < 0.001) and the permanent teeth (P < 0.001), at 7 days post-transplantation. At 4 months post-transplantation the plaque and gingival inflammation score had returned to baseline levels. There were significantly increased mean bacterial plaque and gingival inflammation scores during the period of intense immunosuppression following allogeneic bone marrow transplantation.