Heterosis is a widely studied phenomenon in several plant species. However, its genetic basis still remains to be elucidated. In this study, we used RNA-seq data from two rice genotypes and their reciprocal hybrids, and used a combination of transcriptome profiling and allele-specific expression analysis to identify genes that are differentially expressed in the hybrids and their parents or expressed in an allele-specific manner. The differentially expressed genes (DEGs) were identified by a pairwise comparison of the four genotypes. Detailed annotation of DEGs suggested that these genes showed enrichment in some gene ontology categories, and they tend to have tissue-specific expression patterns compared to all genes. A total of 1033 (10.24%) of 10,195 genes with informative single nucleotide polymorphism (SNPs) were identified as ASE genes. These allele-specific expessed (ASE) genes showed a broader expression breadth suggesting that they function in diverse developmental stages. Among 1033 ASE genes, we also identified 45 ASE transcription factors belonging to 17 transcription factor families. These ASE transcription factors may act in trans to regulate gene expression in filial 1 (F-1) hybrids. Our analyses provide a comprehensive transcriptome profile of rice hybrids and their parents, and would be a useful resource for the rice research community.