Monoamine oxidase A gene (MAOA) has been thought to be a candidate gene implicated in autism spectrum disorder (ASD). This study evaluates the relationship between ASDs and MAOA markers (i.e., uVNTR and four single nucleotide polymorphisms (SNPs)) in 151 Korean family trios with children diagnosed with ASDs, and 193 unrelated Korean controls. The result of case-control global haplotype analysis also showed a statistically significant difference in haplotype frequencies between ASD patients and controls (male d.f.=5, p<0.001; female d.f.=7, p<0.001). With the specific haplotype analyses, the frequencies of the most frequent haplotype (AGG) with three SNPs (rs5906883+rs1137070+rs3027407) in ASD showed significant statistical differences between ASD patients and controls in both the male and female groups (d.f.=1, male p=0.001, female p<0.001). In a family-based association test (FBAT) analysis, it was observed that, in the dominant model, a three-repeat allele of a MAOA-uVNTR marker was preferentially transmitted in ASDs (Z=2.213, p=0.027). Moreover, in the global haplotype analysis, the statistically significant evidence of associations with ASD were demonstrated in additive and dominant models (additive chi(2)=11.349, d.f.=2, p=0.003; dominant chi(2)=6.198, d.f.=2, p=0.045).