The present study was designed to determine the effects of dexmedetomidine on immune function, renal function and inflammatory factors in patients undergoing percutaneous nephrolithotomy under general anesthesia. A total of 177 patients with kidney calculi who underwent percutaneous nephrolithotomy in The Second Affiliated Hospital of Fujian Medical University were enrolled, in which 91 patients were treated with dexmedetomidine during surgery (research group) and 86 patients were not sedated during surgery (control group). The vital signs, renal function, inflammatory factors and immune function during surgery between the two groups were compared. Patients in the research group showed improved vital signs, renal function, inflammatory factors and immune function compared with the control group (P<0.05), and also experienced a significantly shorter hospitalization time (P<0.001). Therefore, the present results suggested that with a relatively high safety profile, use of dexmedetomidine for sedation can effectively protect renal and immune functions, and reduce the inflammatory response of patients during percutaneous nephrolithotomy. Thus, dexmedetomidine may have be potentially applied in clinical practice.