Heterosis describes the superior performance of heterozygous hybrid plants over their homozygous parental inbred lines. Despite the rediscovery of this phenomenon a century ago and its paramount agronomic importance, the genetic and molecular basis of heterosis remains enigmatic. Recently, various pioneer studies described differences in genome organization and gene expression of hybrids and their parental inbred lines. At the genomic level, a significant loss of colinearity at many loci between different inbred lines of maize was observed. At the level of gene expression, complex transcriptional networks specific for different developmental stages and tissues were monitored in maize (Zea mays), rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana). Integration of this complex expression data might contribute to improve our understanding of the molecular basis of heterosis.