Objective: To quantify the association between high-density lipoprotein (HDL) subfractions, efflux capacity, and inflammatory markers at baseline and the effect of supervised exercise on these HDL parameters in patients with peripheral artery disease (PAD)., Methods: The study to improve leg circulation (SILC) was a randomized trial of supervised treadmill exercise, leg resistance training, or control in individuals with PAD. In a post hoc cross-sectional analysis, we quantified the associations between baseline HDL subfraction concentrations (HDL2 and HDL3), HDL-C efflux capacity, and inflammatory markers [C-reactive protein (CRP) and interleukin-6 (IL-6)]. We then examined the effect of supervised exercise on changes in these lipoprotein parameters and inflammatory markers in 88 patients from SILC., Results: Baseline HDL-C efflux capacity was associated with baseline concentrations of HDL2 (β = 0.008, p = 0.0106), HDL3 (β = 0.013, p < 0.0001), and IL-6 (β = -0.019, p = 0.03). Baseline HDL3 concentration was inversely associated with IL-6 concentration (β = -0.99, p = 0.008). Compared to control, changes in HDL2, HDL3, normalized HDL-C efflux capacity, CRP, or IL-6 were not significantly different at 6 months following the structured exercise intervention., Conclusion: HDL efflux and HDL3 were inversely associated with IL-6 in PAD patients. Structured exercise was not associated with changes in HDL subfractions, HDL-C efflux capacity, CRP, and IL-6 in PAD patients. Our preliminary findings support the theory that inflammation may adversely affect HDL structure and function; however, further studies are needed to evaluate these findings.