A major goal in biology is to understand the molecular basis of phenotypic evolution, in particular that of humans and other mammals. Gene expression changes, due to regulatory mutations, are thought to underlie much of phenotypic innovation. Transcriptome studies from us and others based on RNA sequencing (RNA-seq) data for adult organs previously provided initial insights into mammalian gene expression evolution and its phenotypic implications. However, phenotypic evolution is thought to be largely founded on developmental regulatory changes, which determine species-specific tissue morphologies and thus lay the foundation for their typical physiological properties. We therefore added the developmental dimension to our endeavors by generating and analyzing RNA-seq data for more than 2,500 pre- and post-natal developmental samples (ranging from early organogenesis to adulthood) from various organs across representative mammals and an avian outgroup. Based on these data, we have analyzed the evolutionary dynamics of gene expression and phenotypic ramifications for various major aspects of the transcriptome in several projects that include protein-coding gene expression levels, alternative splicing, long noncoding RNAs, microRNAs and sex-biased expression. Overall, these projects provide fundamental novel insights into gene expression evolution and its contribution to the specific organ biology of different mammals, including that of our own species. I will present selected highlights of our endeavors.