Objective: Nonsyndromic cleft lip with or without cleft palate (nsCL/P) is among the most common birth defects, with a birth prevalence of 1/1000 in Caucasians. MSX1 (muscle segment homeobox gene 1) is a strong candidate gene for nsCL/P. The aim of this study was to investigate the association between MSX/ variants and nsCL/P in Turkish patients. Patients and Methods: Our study included 80 patients with nsCL/P and 125 age matched healthy individuals. Genomic DNA was isolated from peripheral blood leukocytes and exon 2 of the MSX1 gene was amplified using polymerase chain reaction (PCR). After PCR, we sequenced the products using an automated sequencer. Results: We found the c.*6C > T variation in the MSX1 gene. This variant in the 3' untranslated region is located 6 bp downstream of the stop codon (TAG) in exon 2. Forty-eight individuals (60%) of 80 in the case group had the CT genotype. We revealed a statistically significant association between the MSX1 c.*6C > T variant and nsCL/P in Turkey (p = 0.01). Conclusion: Our identification of the c.*6C > T variant appears to be the first reported result associating variants of the MSX/ gene with nsCL/P patients.