ABSTRACT The responsible gene of genetic polydactyly/arhinencephaly mouse (Pdn/Pdn) isGli3.Pdn/Pdnexhibits absence of the olfactory bulb, suggesting telencephalic dysmorphogenesis. It has been cleared that a transposon was inserted into intron 3 of theGli3gene in thePdnmouse. Adequate PCR primers in the intron 3 and transposon allowed us to discriminate +/+,Pdn/+ andPdn/Pdnembryos. After genotyping of thePdnembryos using genomic DNA from the yolk sac membrane, gene expressions in the embryo proper were analyzed by DNA microarray, real‐time PCR and whole‐mountin situhybridization (WISH) methods. DNA microarray detected 368 depressed and 425 over‐expressed genes in thePdn/Pdnmouse embryos on day 9 of gestation. In these genes, six signaling pathway and 20 transcription factor genes were included. From these genes, we further investigatedGli3,Emx2,Wnt8bandWnt7bgene expressions using real‐time PCR and WISH, and depression of these gene expression amounts and altered expression patterns were confirmed. Although alterations ofShhandFgf8gene expressions were not detected in the DNA microarray, as these genes have been closed up in the telencephalic morphogenesis, we investigated these gene expressions by real‐time PCR and WISH.Shhgene expression amount and pattern were not changed. Alteration ofFgf8gene expression amount was not detected also in the real‐time PCR, but altered expression pattern was detected in thePdn/Pdnembryos by WISH. From the present data, we suggested thatEmx2,Wnt8b,Wnt7bandFgf8are the importantGli3signaling pathway in the morphogenesis of telencephalon.