Changes in the oral flora and mucosal immunity of 2 groups of children undergoing bone marrow transplantation have been investigated. Patients and methods: Twenty three children received a conditioning regimen of fractionated total body irradiation and chemotherapy (TBI group). A further 11 children received a conditioning regimen of chemotherapy only (CTO group). Both groups were matched with healthy children. Dental indices; Dental caries, plaque and gingivitis scores were recorded. There were significant increases in the scores for dental plaque and gingivitis at 7 days post - transplantation in both the TBI and CTO groups (p < 0.03). Microbiological methods: Saliva was collected on 4 occasions during the peri - transplantation period. Standard microbiological techniques were used for enumeration and speciation of viridans streptococci, Candida, Enterobacteriaceae and enterococci. The most significant changes occurred at 7 days post - transplantation. There were decreases in the mean total aerobic and anaerobic bacterial counts in the TBI group (p < 0.0003 and p < 0.0002) and the CTO group (p < 0.03 and p< 0.009). The proportion of the 'oralis group' of the viridans streptococci as a percentage of the total anaerobic count was increased in the TBI group (p < 0.001) with simultaneous decreases in the isolation frequency of S. parasanguis (p < 0.008), S. sanguis (p < 0.03) and S. salivarius (p < 0.00001). Immunological methods: Total salivary IgA, secretory IgA, total IgG, IgA and antibodies to S. mitis and S. oralis were estimated with ELISA. The main findings were increased salivary IgG at 7 days post - transplantation in both the TBI (p < 0.01) and CTO groups (p < 0.02). Conclusions: The oral flora of children undergoing bone marrow transplantation changed so that they were at increased risk of opportunistic infection from the 'oralis group' during the period of intense immunosuppression.