Emx1 and Emx2 are mouse cognates of the Drosophila head gap gene, ems. Previously we have reported that the dentate gyrus is affected in Emx2 single mutants, and defects are subtle in Emx1 single mutants. In most of the cortical region Emx1 and Emx2 functions would be redundant. To test this assumption here we examined the Emx1 and Emx2 double mutant phenotype. In the double mutants the archipallium was transformed into the roof without establishing the signaling center at the cortical hem and without developing the choroid plexus. We propose that Emx1 and Emx2 cooperate in generation of the boundary between the roof and archipallium; these genes develop the archipallium against the roof. This process probably occurs immediately after the neural tube closure concomitant with the Emx1 expression.