By isolating and identifying the molecular components of the storage material in the ceroid-lipofuscinoses, it should be possible to elucidate the metabolic basis for these diseases. Using brains of English setter dogs afflicted with a form of this disorder, the autofluorescent storage granules have been isolated and subjected to extraction with chloroform-methanol. A significant amount of autofluorescent material was solubilized by this procedure. Spectral analysis of the extracts indicated that the disease-specific fluorophores have corrected fluorescence excitation maxima at 335-340 nm and emission maxima at 530 nm. Analysis of the extracts with thin layer chromatography showed the presence of several disease-related fluorophores. In addition, the amounts of several nonfluorescent lipids appeared to be enhanced as a result of ceroid-lipofuscinosis. A cerebral cortex sample from a human subject who died with the late infantile form of ceroid-lipofuscinosis was subjected to the same analytical procedures. The chloroform-methanol extract from the human brain had a fluorescence spectrum very similar to the extracts from the brains of affected dogs. TLC analysis showed a single fluorophore from the human brain sample. This fluorophore had the same retention time as the most prominent fluorophore present in the samples from affected dogs. These findings are consistent with the possibility that the defects underlying the human and canine ceroid-lipofuscinoses are similar. The analytical procedures established in these experiments are useful in evaluating the various models of ceroid-lipofuscinosis and may ultimately serve as the basis for distinguishing among different forms of these disorders.(ABSTRACT TRUNCATED AT 250 WORDS)