Müllerian ducts are embryonic structures of the female reproductive tract (Fallopian tubes, uterus and upper vagina in mammals, the oviducts in birds). In most vertebrates, embryonic Müllerian ducts initially develop in both sexes, but later they regress in males under the influence of testis-derived Anti-Müllerian Hormone (AMH). While a number of genes or regulatory factors have been implicated in proper duct development and differentiation, many of the molecular details remain obscure. We used RNA sequencing to profile gene expression in the Müllerian duct at key embryonic time points in the chicken embryo; specification (day 4.5/stage 25), invagination (day 5.5/stage 28) and elongation (day 6.5/stage 30). Compared to posterior mesonephros negative control, 234 genes were differentially expressed in the day 4.5 Mullerian duct, 447 at day 5.5 and 610 genes by day E6.5. Gene ontology and pathway analysis indicated that many of these genes encoded proteins involved in extracellular matrix receptor function, Calcium signaling pathway, cell differentiation and migration. Expression of ten novel genes was validated by RT-PCR and whole mount in situ hybridization. These genes were POSTN, SMARCA2, TSHZ3, TGFBI, COL1A2, HTRA3, PRICKLE, LOXL2, FOXE1 and RUNX1. Functional Analysis of some of these genes is being conducted using in ovo electroporation (CRISPR/Cas9 editing). This research will provide new insights into Müllerian duct development and reveal potential new players in Müllerian duct disorders.