Rat embryos with two to four pairs of somites (day 9 of gestation) were examined by scanning electron microscopy and Alcian blue staining. The neural folds, which represent only future brain region at this stage, form a pair of elongated hemispheres with a deep neural groove between them. In transverse section the neural ectoderm is biconvex; the cranial mesenchyme cells beneath them are widely separated by extracellular matrix (ECM) and are joined to each other and to the ectodermal basement membrane by fine cytoplasmic processes and strands of ECM material. In contrast, mesenchyme cells close to the primitive streak are closely packed, having broad areas of surface contact and only small amounts of ECM. The nature and distribution of ECM, cell surface, and basement membrane glycosaminoglycans (GAG) were investigated by staining with Alcian blue at specific pH values in combination with enzyme pretreatments, and at various critical electrolyte concentrations. The results indicate that the GAG of the ectodermal basement membrane, mesenchymal ECM and mesenchymal cell surfaces are in continuity with each other and consist largely of hyaluronate and chondroitin sulphates. Differences in morphology and histochemistry of neural fold and primitive streak regions are discussed in relation to their possible morphogenetic significance.