PAX6 expression was examined during early development of the diencephalon and midbrain of Alligator using an immunocytochemical methodology. These observations focused on the basal plate to determine whether diencephalic prosomere organization in this region followed a pattern previously identified for alar plate areas. PAX6 expression was also described in alar diencephalic regions and the adjacent midbrain. PAX6 (+) cells in the basal plate were first seen in prosomere 1 at stage 7, in the midbrain at stage 10, and lastly in prosomeres 2 and 3 at stage 11. By stage 12, a nearly continuous column of PAX6 (+) cells extended from the midbrain basal plate through the entire diencephalon. In the diencephalon, PAX6 (+) cells in the basal plate were of greatest number in prosomere 1, least in prosomere 2, and intermediate in prosomere 3. This pattern of PAX6 expression distinguished these individual basal plate prosomeres. These results indicate that basal plate prosomeres follow a pattern similar to alar plate prosomereric organization during the later stages of early diencephalon development. Over a comparable time period of early diencephalon development, similar observations have been made in chick basal plate. In Alligator and chick, PAX6 expression in the basal plate is similar in the midbrain and prosomere 1 but different in prosomeres 2 and 3: present in Alligator and absent in chick. In alar plate areas of the Alligator diencephalon, PAX6 expression follows a similar pattern to that described for chick and mouse. These similarities in PAX6 expression in alar diencephalic prosomeres suggest that this is a common feature of amniotes. Differential PAX6 expression in alar prosomere 1 and the midbrain in Alligator is similar to that described for a wide range of species which suggests that these features are common to all vertebrates.