Abstract Background and objective Sickle cell anaemia (SCA) is the most frequent haematological hereditary disease. Children with SCA are submitted to long-term prophylactic therapy with penicillin, but little is known about its impact on oral microflora. The aim of this study was to evaluate the oral microbial colonization of paediatric patients with SCA. Design Forty children (4–11yrs old) with SCA (genotype SS) under long-term prophylactic treatment with penicillin were included in the study. Age/gender-matched control group of healthy children was also included. Scores of dmft/DMFT (number of decayed (D), missing (M), or filled (F) teeth; dmft, for primary dentition; DMFT, for permanent dentition) were obtained and stimulated saliva was sampled. Salivary flow rate and buffering capacity were evaluated. Counts of microorganisms (mutans streptococci, lactobacilli and yeasts) were determined by plating method. Yeasts were identified by API 20C AUX and PCR. Results Mean dmft/DMFT values were similar in the studied groups (SCA 2.13/1.60 and control 2.38/1.3). Although no significant differences between cariogenic microorganism counts were observed, significantly higher yeasts oral levels were observed in SCA group. Controls showed lower salivary buffering capacity. Candida albicans was the most frequently isolated species in both groups. Candida famata, Candida parapsilosis and Candida tropicalis were also isolated from controls. Candida dubliniensis, Candida rugosa and Candida sphaerica were found only in SCA group. Conclusions Based on the results, it could be concluded that paediatric patients with SCA showed significantly higher oral level of yeasts. Uncommon fungal species were found in SCA group. Similar caries prevalence and counts of lactobacilli and streptococci in relation to controls were observed.