HDL exerts anti-inflammatory, antioxidative, and antithrombotic effects in healthy individuals. In this Review, Nosratola Vaziri outlines how HDL structure and function and reverse cholesterol transport is perturbed in patients with nephrotic syndrome, chronic kidney disease, and end-stage renal disease. The underlying mechanisms that contribute to HDL abnormalities and the consequences of these abnormalities, such as progression of cardiovascular complications, are discussed, as well as current treatment options.