This study investigated the oral microbiota of children undergoing liver transplantation. Oral swabs were taken using a standardized procedure from 27 children before liver transplantation and at 3 and 100 days post‐transplantation and from 27 healthy controls at baseline and 90 days. Viridans streptococci, yeasts, staphylococci, enterococci and Enterobacteriaceae were enumerated and identified using conventional techniques. The oral microbiota of the patients changed significantly immediately post‐transplantation, but by the final examination, it had returned to baseline levels. The oral microbiota of the controls did not change significantly. The numbers and proportions of Streptococcus salivarius, Streptococcus sanguis and Streptococcus gordonii as percentages of the total streptococcal counts and of the total anaerobic counts decreased significantly 3 days post‐transplantation (P≤0.006). There were no significant changes in the numbers and proportions of Streptococcus oralis and Streptococcus mitis isolated pre‐ and post‐transplantation. The isolation frequencies and numbers of yeasts were significantly higher in patients than controls. Staphylococci were isolated in low numbers from all children. Enterococci and Enterobacteriaceae were isolated infrequently from patients.