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In briefModes of reproduction across limbed vertebrates are diverse, but the molecular mechanisms required for the development and maintenance of reproductive tract tissue architecture are poorly understood. This paper describes gene expression changes across the regions of the reproductive tract of the adult female brown anole,Anolis sagrei. AbstractThe morphological diversity and functional role of the organs of the female reproductive system across tetrapods (limbed vertebrates) are relatively poorly understood. Although some features are morphologically similar, species-specific modification makes comparisons between species and inference about evolutionary origins challenging. In combination with the study of morphological changes, studying differences in gene expression in the adult reproductive system in diverse species can clarify the function of each organ. Here, we use the brown anole,Anolis sagrei, to study gene expression differences within the reproductive tract of the adult female. We generated gene expression profiles of four biological replicates of the three regions of the female reproductive tract, the infundibulum, glandular uterus, and nonglandular uterus, by RNA-sequencing. We aligned reads to the recently publishedA. sagreigenome and identified significantly differentially expressed genes between the regions using DESeq2. Each organ expressed approximately 14,600 genes, and comparison of gene expression profiles between organs revealed between 367 and 883 differentially expressed genes. We identify shared and region-specific transcriptional signatures for the three regions and compare gene expression in the brown anole reproductive tract to known gene expression patterns in other tetrapods. We find that genes in theHoxcluster have an anterior–posterior, collinear expression pattern as has been described in mammals. We also define a secretome for the glandular uterus. These data provide fundamental information for functional studies of the reproductive tract organs in the brown anole and an important phylogenetic anchor for comparative studies of the evolution of the female reproductive tract.