Autophagy refers to the catabolic processes in eukaryotic cells that deliver cytoplasmic materials to lysosomes for degradation. This highly conserved process is involved in the clearance of long-lived proteins and damaged organelles. Autophagy is important in maintaining cellular homeostasis, providing nutrients to maintain cellular function under starvation, and promoting cell survival under stress, therefore its proper function is important to individual health. Basic lipophilic compounds have been found to accumulate within the lysosome via pH partitioning and perturb lysosomal function. In this study twelve drugs that have previously been shown to accumulate in the lysosome were selected. H9c2 cells were treated with 1.5µM -100.0 µM desipramine, sertraline, fluoxetine, thioridazine, astemizole, chlorpromazine, paroxetine, clomipramine, imipramine, aripiprazole, nortriptyline and chloroquine. Cytotoxicity was evaluated using an ATP depletion assay and autophagy was assessed with LC3 immunofluorescence staining. All twelve drugs induced cytosolic vacuoles and increased staining of LC3. The connection between the increase in autophagosome staining and lysosomal dysfunction was then studied using transcriptomic analysis. Gene expression profiles from all tested drugs revealed a downward trend of expression of plentiful long lived proteins, including structural cytoskeleton and associated proteins, and extracellular matrix proteins, indicating a retardation of protein turnover. Interestingly, various antioxidant response element containing genes, including glutathione S-transferase and NAD(P)H dehydrogenase quinone 1, were upregulated, suggesting activation of the Nrf2 transcription factor. The data in this study indicates that lysosomal accumulation of compounds due to their basic lipophilic nature could contribute to the perturbation of the autophagy process.