Glypicans are essential modulators of cell signalling during embryogenesis. Little is known about their functions in brain development. We show here that mouse glypicans (gpc-1 to gpc-6) are differentially expressed in embryonic brains during key morphogenetic events. In gastrulating embryos, gpc-4 is the only glypican expressed in anterior visceral endoderm. During neural tube closure, gpc-4 transcripts are restricted to the anterior neural ridge and telencephalon. At this stage, gpc-1 expression shifts from trunk and head mesenchyme to neural tube. Gpc-3 mRNA appears across the ventral neural tube, then in the lamina terminalis and hypothalamus. Gpc-2 and gpc-6 transcripts are in all brain compartments. Gpc-5 is found in ventral brains as neurogenesis starts. Onset of neurogenesis also coincides with differential expression of glypican genes either in neural progenitors or in differentiating neurons. The novel expression sites of glypicans shown here contribute to the identification of signalling molecules involved in brain patterning.