Cystatin C and beta-2-microglobulin (B2M) are filtration markers associated with adverse outcomes in non-transplant populations, sometimes with stronger associations than for creatinine. We evaluated associations of estimated glomerular filtration rate from cystatin C (eGFRcys), B2M (eGFRB2M), and creatinine (eGFRcr) with cardiovascular outcomes, mortality, and kidney failure in stable kidney transplant recipients using a case-cohort study nested within the Folic Acid for Vascular Outcome Reduction in Transplantation (FAVORIT) Trial. A random subcohort was selected (N=508; mean age 51.6 years, median transplant vintage 4 years, 38% women, 23.6% non-white race) with enrichment for cardiovascular events (N=306; 54 within the subcohort), mortality (N=208; 68 within the subcohort), and kidney failure (N=208; 52 within the subcohort). Mean eGFRcr, eGFRcys, and eGFRB2M were 46.0, 43.8, and 48.8 mL/min/1.73m2, respectively. After multivariable adjustment, hazard ratios for eGFRcys and eGFRB2M <30 vs. 60+ were 2.02 (95% CI 1.09–3.76; p=0.03) and 2.56 (1.35–4.88; p=0.004) for cardiovascular events; 3.92 (2.11–7.31) and 4.09 (2.21–7.54; both p<0.001) for mortality; and 9.49 (4.28–21.00) and 15.53 (6.99–34.51; both p<0.001) for kidney failure. Associations persisted with additional adjustment for baseline eGFRcr. We conclude that cystatin C and B2M are strongly associated with cardiovascular events, mortality, and kidney failure in stable kidney transplant recipients.