Variations in gene sequence and expression underlie much of human variability. Despite the known biological roles of differential allelic gene expression resulting from X-chromosome inactivation and genomic imprinting, a large-scale analysis of allelic gene expression in human is lacking. We examined allele-specific gene expression of 1063 transcribed single-nucleotide polymorphisms (SNPs) by using Affymetrix HuSNP oligo arrays. Among the 602 genes that were heterozygous and expressed in kidney or liver tissues from seven individuals, 326 (54%) showed preferential expression of one allele in at least one individual, and 170 of those showed greater than fourfold difference between the two alleles. The allelic variation has been confirmed by real-time quantitative PCR experiments. Some of these 170 genes are known to be imprinted, such as SNRPN, IPW, HTR2A, and PEG3. Most of the differentially expressed genes are not in known imprinting domains but instead are distributed throughout the genome. Our studies demonstrate that variation of gene expression between alleles is common, and this variation may contribute to human variability.