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Little is known about the incidence of nephrolithiasis in the United States Navy. Navy pilots must be kidney stone-free and are often referred for treatment of small asymptomatic stones. The primary objectives of this study were to determine the incidence of nephrolithiasis and computerized tomography, proportion undergoing treatment and incidence of stone related mishaps in Navy pilots compared with other Navy personnel.We retrospectively studied the records of all Navy service members from 2002 to 2011 for nephrolithiasis based on ICD-9 stone codes to determine the mentioned rates. We also reviewed NSC (Naval Safety Center) data for a history of accidents associated with nephrolithiasis. Rates of disease were calculated using person-years of followup and inferential statistics were done using univariable and multivariable analyses.We evaluated 667,840 Navy personnel with a total of 3,238,331 person-years of followup. The annual incidence of nephrolithiasis was 240/100,000 person-years with a 5-year recurrence rate of 35.3%. On multivariable analysis pilots had nephrolithiasis incidence and treatment rates similar to those of the overall Navy population. Women had a higher incidence of nephrolithiasis compared with men (OR 1.17, p <0.0001). The rate of computerized tomography was lower in pilots than in the rest of the Navy (39 vs 66/10,000 person-years, p <0.0001). No recorded accidents were associated with kidney stones.Navy pilots had a similar incidence of nephrolithiasis and were no more likely to undergo a surgical procedure. Given that no accidents were associated with nephrolithiasis, this study suggests reconsidering current military policies necessitating pilots to be completely stone-free.