Gene duplications generate genomic raw material that allows the emergence of novel functions, likely facilitating adaptiveevolutionary innovations. However, global assessments of the functional and evolutionary relevance of duplicate genes inmammals were until recently limited by the lack of appropriate comparative data. Here, we report a large-scale study of theexpression evolution of DNA-based functional gene duplicates in three major mammalian lineages (placental mammals,marsupials, egg-laying monotremes) and birds, on the basis of RNA sequencing (RNA-seq) data from nine species and eightorgans. We observe dynamic changes in tissue expression preference of paralogs with different duplication ages, suggestingdifferential contribution of paralogs to specific organ functions during vertebrate evolution. Specifically, we show thatparalogs that emerged in the common ancestor of bony vertebrates are enriched for genes with brain-specific expressionand provide evidence for differential forces underlying the preferential emergence of young testis- and liver-specific expressed genes. Further analyses uncovered that the overall spatial expression profiles of gene families tend to be conserved,with several exceptions of pronounced tissue specificity shifts among lineage-specific gene family expansions. Finally, wetrace new lineage-specific genes that may have contributed to the specific biology of mammalian organs, including the little-studied placenta. Overall, our study provides novel and taxonomically broad evidence for the differential contributionof duplicate genes to tissue-specific transcriptomes and for their importance for the phenotypic evolution of vertebrates.