Autophagosomes and lysosomes are crucial intracellular systems for the regulation of homeostasis. Autophagosomes are responsible for cargo recognition, while lysosomes are responsible for cargo degradation. Lysosomal dysfunction leads to defective degradation of intracellular cargos and accumulation of pathogenic aggregates, which subsequently promotes the pathogenesis of various disorders, including lysosomal storage disorders (LSDs), neurodegenerative diseases and metabolic diseases. Conversely, enhanced lysosome biogenesis and lysosomal function ameliorate human diseases. Therefore, it is an important scientific issue to reveal and elucidate the regulatory mechanisms of lysosome biogenesis. In this article, recent advances in the regulation of lysosome biogenesis are reviewed.