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Abstract Objective: Cleft lip and palate are incomplete development of the lips and palate during the fetus formation. The cariogenic bacteria were significantly increased in cleft lip and palate patients. The aim of this study compared the amount of pre and post-operative bacteria in patients with cleft lip and cleft lip and palate. Methods: This study was an observational laboratory with prospective design study. A sample of 20 people consisting of two groups, 10 people with cleft lips, and 10 people with cleft lip and palate with specified inclusion and exclusion criteria. The sampling of bacteria on the dorsal tongue before and after surgery. Further, bacterial colonies were counted in a laboratory. Processing and data analysis using SPSS version 22 Results: Data analysis showed the statistical differences between pre and postoperative bacteria number, where was in cleft lip patients and cleft lip and palate showed a significant decrease of bacteria number (p <0.05) Conclusion: Pre and post-operative bacterial colonies of the patients with cleft lip and palate were more than cleft lip patients and the number of bacterial colonies was reduced after surgery.