Differential gene expression is a major source of phenotypic diversity and can provide the variation necessary for natural selection. The variable expression of different alleles of the same genes can result from complex regulatory mechanisms. Studying the variable expression of different alleles has been limited by technical challenges in comparing expression of closely related sequences. The implementation of new technologies such as RNAseq has allowed for the study of allelic expression and regulatory variation on a genome-wide scale. The goals of this thesis were to develop methods for studying allele-specific expression and to apply these methods to characterize differential expression of alleles in maize to study the mechanisms underlying two complex examples of gene regulation: genomic imprinting and abiotic stress response. The first set of experiments revealed the prevalence and conservation of imprinting within maize and between maize and other species as well as characterized expression and regulatory differences for imprinted genes. Hundreds of genes exhibit imprinted expression, which is the biased expression of alleles based on parent of origin. Imprinted expression of particular genes is highly conserved in maize, but related genes are rarely imprinted in other plant species. This work also found that examples of maternal and paternally imprinted genes have distinct expression and epigenetic profiles. The second set of experiments provided insights into regulatory variation between maize lines in response to abiotic stress. Substantial variation was observed for steady-state expression levels as well as stress-induced expression changes. Cis- regulatory variation is the predominant regulatory variation pattern for both steady-state and stress-induced expression. By documenting allelic variation for these two cases of complex regulation, imprinting and abiotic stress response, we can begin to understand the mechanisms that underlie this regulation and how complex regulatory variation may evolve.