The aim of the study was to determine the prevalence and bacteriology of bacteremia associated with cleft lip and palate (CLP) surgery. Three venous blood samples were obtained from 90 eligible subjects who presented for CLP surgery: before surgical incision, 1 minute after placement of the last suture, and 15 minutes thereafter. The samples were injected into an Oxoid Signal blood culture and transported to the laboratory for gram-positive/negative and aerobic/anaerobic bacteria analysis. Prevalence of bacteremia associated with cleft surgery was 38.1%. Prevalence rates of bacteremia in cleft lip surgery, cleft palate surgery, and alveoloplasty were 40.9%, 33.3%, and 50%, respectively. There was no significant difference in prevalence rate of positive blood culture in cleft lip surgery, cleft palate surgery, and alveoloplasty (P = 0.69). Positive blood culture was detected most frequently (47%) 1 minute after placement of the last suture. Of the 23 subjects who had positive blood culture at 1 minute, bacteremia persisted in 8 (35%) of them after 15 minutes. The most common bacteria isolated were coagulase-negative staphylococcus, Acinetobacter lwoffii, and coagulase-positive Staphylococcus aureus. Sex and age of the subjects, duration of surgery, blood loss, and type of cleft surgery were not significantly associated with positive blood culture. Bacteremia associated with CLP surgery is polymicrobial and persisted for at least 15 minutes after surgery in 35% of cases. This may reinforce the need for prophylactic antibiotics to protect at-risk patients from developing focal infection of the heart by oral flora.