Enabled by high-throughput technologies that are capable of generating millions of sequencing reads, transcriptome sequencing is emerging as an important approach for mapping allelic imbalance (AI), where transcription is biased toward one allele in a diploid system. AI is identified by counting sequencing reads that map to genomic regions containing heterozygous SNPs, where the base identity of the SNP is used to distinguish allelic origin. Genomic imprinting is a special case of AI where bias is toward parental sex and can be identified by transcriptome sequencing of systems that represent reciprocally inherited loci. The focus of this protocol is on experimental design, analysis, and interpretation of genomic imprint discovery using whole transcriptome sequencing.