Objective Allelic expression imbalance (AEI) assays are a sensitive method for detecting genetically regulated expression of mRNAs in human tissues.Based on these measurements, it is often possible to identify common regulatory variants that contribute to susceptibility to complex diseases.The goal of this study is to develop a novel high-throughput AEI assay for measuring mRNA expression of neuropsychiatric disorder candidate genes in human brain.Methods In this study, we examined allele-specific mRNA expression for 71 candidate genes for schizophrenia, Alzheimers disease, and/or heroin addiction in 52 samples of postmortem human brain.We used gene-specific PCR primers to amplify short segments of cDNA that contain a "marker" single nucleotide polymorphism (mSNP) that permits mRNA transcribed from each genetic allele to be distinguished.After ligation to indexed adapters to allow the sorting of DNA sequences according to sample of origin, we carried out deep sequencing of the PCR products using next generation DNA sequencing technology (Illumina Genome Analyzer 2.0).AEI ratios for mRNA expression were calculated from the number of sequencing reads for each gene in each independent sample.Results Among the 71 genes analyzed, 54 (76%) showed significant AEI in at least 10% of the samples.Arranging log2AEI ratios for each gene in increasing order produced AEI "population profiles" that were distinct for each gene/mSNP pair.Based on mathematical modeling, we discovered that these population profiles yield important information about the number, location and contributions of cis-acting regulatory variants to mRNA expression.Conclusion We have developed a reliable and sensitive high-throughput method to analyze AEI of mRNA expression in human brain.This method has the capacity to measure 100-to 200-genes in 100 samples in a single experiment.This is a suitable scale for investigating sets of complex disease candidate genes, such as genes that function in specific biological pathways that contribute to neuropsychiatric disorders.