Single nucleotide polymorphisms (SNPs) are important markers which can be used in the association study for searching for associated genes of complex diseases. High-throughput methods in a large number of samples are needed for SNP genotyping. In this study, we applied polyacrylamide gel-based microarray combined with universal dual-color hybridization for trios-based associative study of BDNF polymorphisms with autism in Chinese. All four SNPs in both patients and their parents could be analyzed quickly and correctly. In single SNP TDT analysis, C270T showed preferential transmission of the T allele compared to the C allele (TDT p < 0.001) in autism. In haplotype TDT analysis, C270T polymorphism also existed in the haplotype combination which showed significant association (TDT p < 0.05). These results suggest a potential association between BDNF and autism in the Chinese population. The study also show that the polyacrylamide gel-based microarray combined with universal dual-color detectors is a rapid, simple, high-throughput method for SNPs genotyping, and can be very effective and cost effective in association study of susceptible gene with disorders in large samples.