The dorsal and ventral domains of the telencephalon are delineated by a unique boundary structure that restricts the migration of dorsal and ventral cells to a different extent. While many cells invade the dorsal cortex from the ventral ganglionic eminence (GE), hardly any cortical cells cross the boundary into the GE. Several molecules have been implicated in the regulation of ventral to dorsal cell migration, but so far nothing is known about the molecular mechanisms restricting cortical cell migration in vivo. Here we show that in the absence of the transcription factor neurogenin 2, cells from the cortex migrate into the GE in vitro and in vivo as detected in transgenic mice containing a lacZ gene in the neurogenin 2 locus. In contrast, the migration of cells from the GE is not affected. Molecular and cellular analysis of the cortico-striatal boundary revealed that neurogenin 2 regulates the fasciculation of the cortico-striatal boundary which may explain the non cell-autonomous nature of the migration defect as detected by in vitro transplantation. Taken together, these results show that distinct cues located in the cortico-striatal boundary restrict cells in the dorsal and ventral telencephalon.