Swelling of rat liver mitochondria induced by various neutral amino acids indicates that the L isomers of serine, alanine, methionine, valine, threonine, and leucine enter the mitochondrial matrix by a stereospecific process. Chemical modification of mitochondria with diazobenzenesulfonate or p-mercuribenzoate inhibited the rapid uptake of these compounds, as well as that of L-proline and glycine, to various extents. Diazobenzenesulfonate did not inhibit the transport of compounds that enter the mitochondrial matrix by simple diffusion, i.e., thiocyanate, nitrate, formate, bicarbonate, and acetate. Inhibition by p-mercuribenzoate was reversed by treatment with dithiothreitol. Inclusion of various neutral amino acids in the p-mercuribenzoate preincubation mixture substantially prevented inactivation of transport. Glycine, D- or L-serine, L-threonine, L-methionine, L-alanine, and L-valine all individually protected against the inactivation of glycine, L-serine, L-threonine, L-methionine, L-alanine, L-valine, L-proline, and beta-alanine transport, while L-proline, beta-alanine,