OBJECTIVE: We compared arterial stiffness and heart rate variability (HRV) over time by diabetes type and determined the risk factors associated with worsening arterial stiffness and HRV in young adults with youth-onset diabetes. RESEARCH DESIGN AND METHODS: Arterial stiffness (pulse wave velocity, augmentation index) and six indices of heart rate variability were measured twice, 4.5 years apart, among participants with either youth-onset type 1 or type 2 diabetes in the SEARCH for Diabetes in Youth study. Multivariable linear regression models were used to assess risk factors associated with arterial stiffness and HRV at follow-up. RESULTS: Of 1,159 participants studied, 949 had type 1 diabetes (mean age 17.1 +/- 4.7 years, 60.3% non-Hispanic White, 55% female) and 210 had type 2 diabetes (mean age 22.1 +/- 3.5 years, 23.8% non-Hispanic White, 71% female) at initial assessment when diabetes duration was 7.9 years (both groups). Participants with type 2 versus type 1 diabetes had greater arterial stiffness and more abnormalities in HRV at initial and follow-up assessment and a greater change over time (all P < 0.05). Risk factors associated with worse arterial stiffness and HRV at follow-up in both types of diabetes included higher blood pressure, hemoglobin A1c, waist circumference, and triglycerides over time and longer diabetes duration. CONCLUSIONS: Arterial stiffness and HRV worsened over time with greater changes among participants with type 2 versus type 1 diabetes and among those with features of the metabolic syndrome. The risk factor profile documents potentially modifiable pathways to prevent or limit cardiovascular complications in young adults with youth-onset diabetes.