The endosomal/lysosomal system is essential for cell survival. The regulation of lysosomal pH is critical for lysosomal function and has been known to play a pivotal role in aging and disease. The pH within the lysosomes is essentially increased in certain diseases and our preliminary data suggests that it may also increase with age. It is known that the methods used for lysosomal pH measurement are extremely difficult and technique sensitive. In this study, we searched for key genetic markers to help identify the presence of chronic elevation of lysosomal pH. This will allow us to utilize the speed, specificity and sensitivity of laboratory confirmation with quantitative polymerase chain reaction (qPCR) as an alternative method to direct measurement of lysosomal pH. In our study, we demonstrated a trend towards an increased expression of TcfEB and vATPase genes in the presence of long-term lysosomal pH elevation. Therefore, these two genes could potentially be used as markers to recognize the presence of chronic lysosomal pH elevation in diseased cells. In contrast, a short-term lysosomal pH elevation showed a decreased expression of IL-1b, IL-18 and TcfEB highlighting the time-dependent nature of genetic expression. Both genes, TcfEB and vATPase, might be used as important tools for the rapid detection of disease or infection in clinical specimens and are also particularly suitable in optimizing the therapeutic management of diseased cells.