Glutamine transport was studied in submitochondrial particles (SMP) to avoid interference from glutamine metabolism. Phosphate-dependent glutaminase activity in SMP was only 0.04% of that in intact mitochondria. The uptake of glutamine in SMP represented both the transport into vesicles and membrane binding (about one-third of total uptake). Sulfhydryl reagents inhibited glutamine uptake in SMP. The uptake of L-[3H]glutamine increased more than twofold in SMP preloaded with 1 mM L-glutamine, an effect that was not seen with 1 mM D-glutamine. The uptake of L-[3H]glutamine was inhibited in the presence of either L-glutamine or L-alanine in the incubation medium. Other amino acids did not inhibit glutamine uptake. Alanine was also shown to trans-stimulate glutamine transport in SMP and cis-inhibit glutamine transport in both SMP and intact mitochondria. Glutamine transport showed a positive cooperativity effect with a Hill coefficient of 1.45. Metabolic acidosis increased the affinity of the transporter for glutamine without any change in other kinetic parameters. These data indicated that mitochondrial glutamine transport occurs via a specific carrier with multiple binding sites and that the transport of glutamine into mitochondria has an important role in increased ammoniagenesis during metabolic acidosis.