The genetic polydactyly/arhinencephaly mouse (Pdn/Pdn), whose responsible gene is Gli3, has been considered to be a mouse homolog of Greig cephalopolysyndactyly syndrome (GCPS), which is induced by mutation of GLI3. Recently, mutation point of Pdn mouse was demarcated, that is, a transposon was inserted into intron 3 of the Gli3 gene. Adequate PCR primers were constructed in the intron 3 and transposon. Now we can discriminate +/+, Pdn/+, Pdn/Pdn embryos from the PCR products. After genotyping of the Pdn embryos, Gli3 and other correlated gene expressions were analyzed by DNA microarray, Real Time PCR and whole-mount in situ hybridization methods. Suppression of Gli3 gene expression was detected in Pdn/Pdn embryos by Real Time PCR methods.