Two lysosomal storage diseases are now known to result from impaired transport of small molecules across the lysosomal membrane. In cystinosis, the disulfide amino acid, cystine, accumulates and in free sialic acid storage disorders, N-acetylneuraminic acid is stored. The lysosomal cystine carrier exhibits saturability, counter-transport, temperature dependence, and stereospecificity; it is highly specific for molecules resembling cystine. Less is known about sialic acid transport, but its temperature dependence and deficiency in certain autosomal-recessive human mutations strongly suggests that it is a carrier-mediated process. Cystine and sialic acid serve as prototypes for amino acids and sugars transported by specific lysosomal membrane carriers, whose impairment results in lysosomal storage disorders.