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<h4>Background</h4>Myelin transcription factor 1-like (MYT1L) is a member of the myelin transcription factor 1 (MYT1) gene family, and the neural specific, zinc-finger-containing, DNA-binding protein that it encodes plays a role in the development of the nervous system. On the basis of a recent copy number variation (CNV) study showing that this gene is disrupted in mental disorder patients, we investigated whether MYT1L also plays a role in MDD.<h4>Methods</h4>In this study, 8 SNPs were analyzed in 1139 MDD patients and 1140 controls of Chinese Han origin.<h4>Results</h4>Statistically significant differences were noted between cases and controls for rs3748989 (allele: permutated p = 0.0079, corrected p = 0.0048, genotype: corrected p = 0.0204). A haplotype of rs1617213 and rs6759709 G-C was also significant (permutated p = 0.00007).<h4>Conclusion</h4>Our results indicate that MYT1L may be a potential risk gene for MDD in the Chinese Han population.