Extracellular glycosaminoglycans (GAG) were examined in embryonic rat valvular primordia (cushion tissue) to determine if there are specific, in situ, intermolecular associations of GAG and if the passage of migrating cushion cells alters matrical organization. Precursor incorporation studies and colloidal iron staining controlled by acidified methylation, pH, and polysaccharidase digestion indicated that both hyaluronate (HA) and chondroitin sulfate (CHS) were secreted into the premigratory matrix with the predominant GAG being HA. Premigratory matrix was revealed by scanning electron microscopy after routine fixation as a microfibrillar stroma; addition of cetylpyridinium chloride (CPCL) to the fixative resulted in the retention of an additional matrical component superimposed upon the microfibrillar stroma. TEM analysis of the CPCL-dependent matrix revealed that it was composed of intertwined 3-nm filaments, electron-dense, amorphous material, and 30-nm granules. Collagen-like microfibrils were associated primarily with the filamentous component of the CPCL-dependent matrix. Ultracytochemical results obtained with dialyzed iron binding regulated by pH and polysaccharidase and protease digestion suggests that the 3-nm filaments contain HA and the granules contain both CHS and protein. Commensurate with cushion cell formation and migration, X-ray dispersive analysis and polyanionic histochemical criteria indicated increased deposition of CHS in the postmigratory matrix (i.e., matrix transversed by cells). Ultrastructurally, the CPCL-dependent components of the postmigratory matrix became progressively restructured within the wedge of migrating cells. In contrast to premigratory matrix, fewer 3-nm filaments were evident, while 30-nm granules heavily studded the collagen-like microfibrils. Physical fixation controls confirmed the variations between pre- and postmigratory matrices. These results suggest that modification in the matrix organization of embryonic heart GAG may be correlated with the migration of cushion tissue mesenchyme.