Objective: Obesity is an independent risk factor for chronic kidney disease. Bariatric surgery is effective for improvement of clinical parameters of the kidney in obese patients. Recently, urinary mitochondrial DNA (mtDNA) has been used as a surrogate marker of mitochondrial damage in various kidney diseases. However, there are no data regarding its use in obese patients who require bariatric surgery and the change in urinary mtDNA copy number after surgery. Methods: We prospectively recruited age- and sex-matched healthy volunteers and obese patients who were scheduled to undergo bariatric surgery (n = 22 in each group, 8 men and 14 women). The copy number of urinary mtDNA nicotinamide adenine dinucleotide dehydrogenase subunit-1 (mtND-1) in a 24-hour urine sample was measured by quantitative polymerase chain reaction. Changes in urinary mtND-1 copy number, body weight, blood pressure, and laboratory measurements including kidney injury marker were evaluated 6 months after bariatric surgery. Results: Urinary mtND-1 copy number was significantly higher in the group of obese patients (median 221 100 copies/μL of urine/nuclear DNA [nDNA], interquartile range [IQR] 92 550-922 000, P < 0.001) than in healthy volunteers (median 83 400 copies/μL of urine/nDNA, IQR 76 400-179 850). When obese patients were divided into two groups according to their baseline mtND-1 copy number, it was observed that bariatric surgery reduced mtND-1 copy number (P = 0.006) in the high baseline mtDNA copy number group but not in the low baseline mtDNA copy number group (P = 0.182). The change in urinary mtND-1 copy number correlated with the change in urinary albumin (r = 0.478, P = 0.025). Conclusion: Obesity is associated with elevated urinary mtND-1 copy number. Bariatric surgery reduces elevated urinary mtND-1 copy number in obese patients. This suggests that bariatric surgery would improve mitochondrial damage in the kidney cells of morbidly obese patients.