Introduction: Cystinosis is a lysosomal storage disease caused by mutations in the CTNS gene (17p13), encoding the lysosomal cystine transporter cystinosin. Nephropathic cystinosis is characterized by the development of generalized proximal tubular dysfunction during infancy or childhood, progressing towards end-stage renal disease around the age of 10 in untreated patients. Extrarenal organs including the eyes, thyroid gland, endocrine and exocrine pancreas, liver, muscles, central and peripheral nervous system are also affected by the disease, mostly at later age. The pathogenesis of cystinosis is still incompletely understood. Treatment strategies are focused, on the one hand, on the replacement of renal losses and endocrine deficiencies and, on the other hand, on lowering cystine accumulation by the administration of cysteamine. Cysteamine is of major importance for protecting kidneys and extrarenal organs; however, this treatment is not curative and has multiple side effects thus hampering the compliance. Areas covered: This article describes main clinical features of cystinosis and provides an overview of currently available and experimental treatments. Expert opinion: Based on the recent advances towards a better understanding, the disease mechanism and improving treatment, novel research targets are discussed.