Background: Persons with morbid obesity are at increased risk for end-stage kidney disease, and prior studies have shown an association between bariatric surgery and improvements in creatinine-based estimated glomerular filtration rate (eGFR cr ). However, eGFR cr could be biased by loss of muscle mass after surgery, and creatinine-cystatin C estimated glomerular filtration rate (eGFR cr-cyc ) has been shown to be more accurate in this setting. Methods: We matched 144 patients who underwent bariatric surgery on pre-surgery age, sex, race, body mass index (BMI), and eGFR cr with 144 morbidly obese non-surgery patients at Geisinger with serial biobanked serum samples. We measured filtration markers (creatinine, cystatin C, beta-2 microglobulin [B2M] and beta-trace protein [BTP], and calculated eGFR cr-cyc using the CKD-EPI combined equation. Using mixed effects models with random intercepts, we compared changes in filtration markers and eGFR cr-cyc between surgery and non-surgery groups. Results: Mean (SD) values for age, BMI, and eGFR cr were 48.2 (10.4) years, 45.2 (6.3) kg/m 2 , and 91.7 (17.5) ml/min/1.73m 2 ; 87.5% were female, 0.7% were black, 50.3% had hypertension, and 41.0% had type 2 diabetes. Mean eGFR cr-cyc slope in the surgery group was -0.41 ml/min/1.73m 2 /yr (95% CI: -0.74, -0.08) over a mean follow-up of 9.2 (1.4) years, compared to -1.43 ml/min/1.73m 2 /yr in the non-surgery group over a mean follow-up of 8.2 (1.1) years. Bariatric surgery was associated with a 1.02 ml/min/1.73m 2 /yr slower decline in eGFR cr-cyc , and smaller increase in all 4 filtration markers (p< 0.02 for all comparisons). Conclusions: Bariatric surgery is associated with slower decline in kidney function, as assessed by eGFR cr-cyc , B2M and BTP.