The aim of this investigation was to evaluate the prevalence of Candida and Enterobacteriaceae in a group of adolescents during fixed orthodontic appliance (FOA) therapy. The experimental group was recruited from a larger sample of orthodontic patients who were clinically examined once to obtain baseline data before active treatment. The group comprised 27 subjects; 13 males, 14 females (mean age 15.5 +/- 2.3 years). Thereafter, the experimental group was examined three times during a 3 month follow-up period after insertion of the FOA. The whole mouth plaque score was obtained, and the oral cavity was then sampled for Candida species and Enterobacteriaceae using three different microbiological culture techniques, namely the oral rinse, pooled plaque and the imprint culture.A significant increase in candidal numbers was observed after FOA insertion when the imprint technique was used (P < 0.001), although the overall candidal prevalence rates obtained using the oral rinse and pooled plaque techniques did not demonstrate such a change. The predominant Candida species isolated was C. albicans and the number of coliform carriers significantly increased after the insertion of a FOA, as detected by the oral rinse (P < 0.05) and the pooled plaque (P < 0.05) techniques. In total, eight coliform species were isolated following FOA therapy compared with the three species isolated before insertion of the appliance. The results also revealed a significant increase in plaque index due to the introduction of a FOA. Taken together, these data imply that insertion of a FOA is likely to promote oral carriage of Candida and coliform species. Furthermore, it appears that routine oral hygiene instruction and information on appliance hygiene given to these patients may not necessarily reduce plaque accumulation and possible attendant effects. Further work with a larger cohort is required to confirm these findings.