Aminoglycoside antibiotics cause phospholipid accumulation in the kidney proximal tubule cell by inhibiting phospholipid catabolism in lysosomes. To evaluate the mechanism of inhibition, we purified lysosomal phospholipase A1 from rat kidney and examined the effects of gentamicin and tobramycin on the hydrolysis of di-[1-14C]oleoylphosphatidylcholine alone or in the presence of unlabeled phosphatidylinositol. Gentamicin and tobramycin were weak inhibitors of phospholipase A1 action with dioleoylphosphatidylcholine as substrate; the amount of drug required to reduce hydrolysis by 50% was greater than 10 mM. However, when unlabeled phosphatidylinositol was present in the liposome, gentamicin and tobramycin caused 50% inhibition at 0.03 or 0.01 mM, respectively, a decrease of more than three orders of magnitude. When the concentration of phosphatidylinositol-containing vesicles was increased, inhibition by aminoglycosides could be overcome. The results are consistent with the previously demonstrated ability of gentamicin and tobramycin to bind to liposomes containing negatively charged phospholipids which, in turn, may interfere with phospholipase A1 degradation of phosphatidylcholine. Inhibition by the substrate depletion mechanism has been reported previously with lipocortin/calpactin where binding of these proteins to the surface of substrate vesicles results in a substrate depletion type of inhibition. The mechanism of aminoglycoside inhibition of phospholipase A1 appears to be a variant of this phenomenon in which the polycationic drugs bind to phosphatidylinositol, a nonmetabolized component of substrate vesicle, preventing productive interaction of the enzyme with the phosphatidylcholine substrate.