Background: Increased urinary exosomes are associated with kidney stones but how they work is unknown. In this study, we aim to identify dysregulated proteins in urinary exosomes from kidney stone patients and to explore the potential role of exosomal proteins in nephrolithiasis. Methods: First morning voids were collected from participants. Urinary exosomes were isolated via ultracentrifugation. Label free liquid chromatography-tandem mass spectrometry was performed to analyze the proteome of urine exosomes from three kidney stone patients and three age-/sex-matched healthy controls. Bioinformatics analysis was conducted to identify dysregulated proteins associated with stone formation. Results of proteomic analysis were verified by Western blotting in other three kidney stone patients and three healthy controls. Results: Nine hundred and sixty proteins were identified with proteomic analysis, of which 831 were identified in the control group and 879 in the stone group. Sixteen proteins in urinary exosomes were found most significantly different between kidney stone patients and healthy controls. Gene ontology (GO) analysis showed that dysregulated proteins were enriched in innate immune response, defense response to bacterium and calcium-binding. S100A8, S100A9 and S100A12 were common in above three GO terms and were chosen for further study. Western blotting confirmed that the expression of these three S100 proteins was higher in urinary exosomes from kidney stone patients. In addition, S100 proteins were aggregated in urinary exosomes and it was difficult to detect them in urine. Conclusions: Urinary exosomes from kidney stone patients are rich in S100 proteins and play a role in innate immune response, defense response to bacterium and calcium-binding.