Lhx2/9 and Etv1 transcription factors have complementary roles in regulating the expression of guidance genes slit1 and sema3a.

•lhx2/9 are expressed in the forebrain, in complementary domains to slit1/sema3a.•etv1 mRNA expression coincides with mRNA expression of slit1 and sema3a.•Lhx2 is an indirect repressor of these guidance genes while Etv1 is an activator.•Lhx2/9 and Etv1 may regulate the levels and boundaries of slit1/sema3a expression.