There is little information on the microbiology of periapical lesions, and no data on the residual microbial flora in the periapex, if any, after apicoectomy procedures. Hence, 64 patients treated by apicoectomy procedures were prospectively studied to assess the bacterial flora in the periapex and to evaluate the residual bacteria in postoperative apicoectomy sites. Of the 64 lesions studied, 14 (22%) were sterile and 50 (78%) yielded bacteria preoperatively. Bacteria could be recovered from 28 (56%) of the latter lesions after apicoectomy and curettage. A total of 105 bacterial strains was isolated from 50 lesions, yielding a range of 1-4 (mean 2.1) species per sample. The isolates comprised 84 (80%) facultative anaerobes and 21 (20%) strict anaerobes. A polymicrobial growth was obtained from 39 lesions whilst 11 lesions yielded pure cultures. On detailed microbiological analyses of 29 lesions, 40% of the isolates were identified as alpha-haemolytic streptococci, half of which were Streptococcus sanguis; anaerobic streptococci were the predominant anaerobes. None of the organisms or group(s) of organisms emerged as recalcitrant colonisers which were difficult to dislodge after surgical debridement. These data indicate that the majority of periapical lesions harbour a variety of flora which cannot be eradicated despite thorough apicoectomy procedures.