AIMS: To determine: (i) the relative prevalence and diversity of yeasts in salivary and root canal samples from the same patients; and (ii) the clinical factors associated with their presence in saliva and root canals. METHODOLOGY: Sixty root canal samples from teeth associated apical periodontitis and the corresponding whole unstimulated saliva samples were obtained from 55 patients. The medical history including antibiotic therapy and clinical/radiographic data on the teeth were recorded. The samples were serially diluted and cultured on yeast & fungi-selective sabouraud dextrose agar. Isolates were characterized and speciated by the germ tube formation test, hyphal morphology and a commercial biochemical test kit (Rapid ID32C(R) system). RESULTS: Twenty-three yeast isolates were recovered from 19 saliva samples and eight isolates from six root canal samples. Candida albicans (17/23 & 3/8) and Rodotorula mucilaginosa (2/23 & 4/8) were the most prevalent isolates from saliva and root canal samples. It was significantly (13.8 times) more probable that yeasts would be recovered from root canals when they were also present in the saliva (P = 0.021). The effect of coronal restoration leakage (P = 0.08) and previous root canal treatment (P = 0.123) were equivocal. The history of antibiotic therapy had no association with the presence of yeasts in saliva (OR = 1.1). CONCLUSIONS: Yeasts occurred relatively infrequently (10%) in root canals. Their presence in root canals was significantly associated with their presence in saliva. The role of yeasts in the initiation and perpetuation of periapical disease remains to be determined.