Mammals exhibit a remarkable diversity in organ morphology and physiology. Identifying the genetic and developmental bases of this diversity will greatly advance our understanding of phenotypic evolution and the developmental and evolutionary underpinnings of human disease. Gene expression provides a molecular read-out of developmental processes and therefore a window into the genes and regulatory networks underlying organ development. I will describe a new evo-devo resource consisting of developmental gene expression time series for seven major organs (cerebrum, cerebellum, heart, kidney, liver, ovary and testis) from early organogenesis to adulthood for human, rhesus macaque, mouse, rat, rabbit, opossum and chicken. Using the developmental time series we established stage correspondences for all species throughout development, which provided the basis for evolutionary comparisons and revealed pronounced heterochronies in the gonads. We found that although globally, developmental programs are conserved across mammals, the conservation is not uniform across organs and that it notably changes throughout development. Species transcriptomes are most similar at the earliest developmental stages and then progressively diverge. This matches the increase in morphological divergence observed between species with developmental time described by von Baer already in the 19th century. We find evidence that this pattern is driven by the high pleiotropy of the genes employed early in development, which imposes strong constraints on evolution. As organs differentiate and mature, the genes employed have increasingly lower pleiotropy, thereby decreasing constraints and increasing the opportunities for evolutionary change. Evolutionary change is driven by the deployment of lineage-specific genes and by the evolution of new developmental trajectories in pre-existing genes. We identify hundreds of genes with novel developmental trajectories in each of the organs, which are strong candidates for underlying lineage-specific morphological and physiological phenotypes. Our work furthers our understanding of the genetic and developmental foundations of the evolution and phenotypic diversity of mammals.