Twenty patients with residual clefts or pronounced soft tissue grooves, treated for uni- or bilateral cleft lip, alveolus, and palate were included in this study. Ten patients were recalled for dental prophylaxis at regular intervals, 10 patients were not. One microbiologic sample was obtained from the cleft area and two samples from a tooth adjacent to the cleft (sites adjacent and distant to the cleft). Between the recall and the nonrecall group there were notable differences in the presence of anaerobic Gram-negative organisms. Fusobacterium spp., Prevotella melaninogenica, and P. intermedia were more often found in nonrecall patients. While rarely seen in recall patients, spirochetes and motile rods were a common feature of nonrecall patients. The putative periodontal pathogens Actinobacillus actinomycetemcomitans and Porphyromonas gingivalis were not detected in either group. The differences between the recall and the nonrecall groups were more pronounced when the respective samples from teeth were related to each other than when the samples obtained from the clefts were compared. The cleft flora was less complex irrespective of how good maintenance was and resembled the flora of teeth of well-maintained patients. Samples from clefts were never Wolinella positive, and harbored significantly less Capnocytophaga and Actinomyces viscosus than samples from dental sites.