Objectives. Compare the total salivary Streptococci and Lactobacilli counts in cleft and noncleft children with differing caries experiences, correlate the bacterial counts with dmft/DMFT status and identify the different biotypes of Mutans Streptococci (MS). Patients. Group I included thirty subjects with dental caries (DC) and cleft lip and palate (CL/P); Group II had thirty subjects with DC but without CL/P. Group III comprised a control of thirty subjects with neither DC nor CL/P. Methodology. Enumeration of total salivary Streptococci and Lactobacilli was done by the plate count method and correlation of counts with dmft/ DMFT status examined. Differences in biochemical reactions were used to identify the biotypes. Results. Streptococci colonies in CL/P children with caries (64.30 ± 24.52) was significantly higher than in children with no CL/P or caries (45.57 ± 16.73). No significant differences in the Lactobacilli count were observed. dmft/DMFT status and Streptococci counts showed a strong positive correlation whereas Lactobacilli counts showed a moderate correlation. S. mutans was the predominant biotype. Conclusions. Higher total salivary Streptococci and Lactobacilli counts exist in cleft subjects with caries than in the non-cleft subjects. Positive correlation between dmft/DMFT scores and salivary Streptococci reinforces its role in DC. S. mutans and S. sobrinus are the biotypes more frequently associated with dental caries in children.