Background: In the search of the major genes responsible for the genetic etiology of Nonsyndromic Cleft Lip and Palate (NSCLP), an association study between this malformation and four molecular markers, F13A1 and EDN1 (6p), D17S579 (17q) and BCL3 (19q), was done. Aim: To determine, in a Chilean population, the presence of NSCLP susceptibility regions, as proposed for Caucasian populations in the 6p, 17q and 19q chromosomal regions. Material and Methods: A sample of unrelated NSCLP patients, that belonged to Simplex (Sx) and Multiplex (Mx) families, was analyzed. Blood donors were used as a control group (Co). The DNA of the four markers was amplified by means of PCR, their products analyzed by PAGE denaturants and visualized by silver staining. Statistical analysis was performed using χ2 log ratio. Results: Allele frequency distribution of D1 7S579 was significantly different in all patients with NSCLP and their subgroups, when compared to control subjects. Significant differences in EDN1 frecuency were observed between the total groups of NSCLP patients and those pertaining to the Mx subgroup, when compared to controls. Differences in F13A1 distribution were only observed between NSCLP-Mx patients and controls. There was a slight difference in BCL3 distribution, between the total sample of NSCLP patients and controls. Conclusions: Our results support the hypothesis of the existence of cleft susceptibility regions in 6p and 17q. The small significance of BCL3, suggests that ethnicity can influence the interactions between involved genes.