Advances in molecular and computational biology in recent years have led to the development or the improvement of methods for analyzing global gene expression. In most of these efforts, it is assumed that alleles of different origins contribute equally to the transcript pool. However, accumulating evidence suggests that many genes are not equally expressed from the paternal and maternal chromosomes. In addition to imprinting, the phenomenon of imbalanced allelic expression is widespread in heterozygous individuals. To distinguish transcript pools derived from different alleles present in the same organism, a number of methods have been developed. Here, we describe an oligonucleotide tiling microarray-based assay for analyzing allele-specific gene expression. Specifically targeting single-nucleotide polymorphisms, this two-step assay offers a high-throughput and multiplex method for detecting and quantifying unequal allelic expression that is readily applicable to many experimental systems.