OBJECTIVE: To evaluate the association between MSX1 CA polymorphism and nonsyndromic cleft lip with or without cleft palate (CL+/-P) in a group of patients from Operation Smile Colombia. DESIGN: Four alleles from MSX1 CA microsatellite sequence were analyzed. Polymerase chain reaction was carried out. The amplifications were performed by Short Tandem Repeats (STRs) in ABI PRISM 310 genetic analyzer. Chi-square and odds ratio tests were used to determine the association between genotype frequencies and the risk to the cleft lip/palate in a Colombian group population. SETTING: Operation Smile Colombia. PARTICIPANTS: Ninety-four affected patients (49 men and 45 women with CL+/-P) and 93 control individuals (43 men and 50 women). RESULTS: A significant statistical difference (p<.0106) was found between the patients who carried allele 3 and CL+/-P. In addition, allele 4 (heterozygous and homozygous form) was the most frequent in CL+/-P (74%) patients and in the control group (82%). CONCLUSIONS: These findings show a positive association between the MSX1 CA polymorphism and CL+/-P in a Colombian group population.