Secondary hyperparathyroidism (HPT) is a common complication of chronic kidney disease (CKD) that can lead to clinically significant bone disease. Additional consequences of secondary HPT, such as soft-tissue and vascular calcification, cardiovascular disease, and calcific uremic arteriolopathy, may contribute to the increased risk of cardiovascular morbidity and mortality among CKD patients. Secondary HPT arises from disturbances in calcium, phosphorus, vitamin D and parathyroid hormone metabolism, which develop early in the course of CKD and become more prominent as kidney function declines. The standard therapies currently recommended to correct mineral metabolism and bone disease in these patients include calcium supplementation, dietary phosphorus restriction, phosphate-binding agents, and treatment with vitamin D sterols. However, such medications often have significant effects on the serum levels of calcium and phosphorus, which result in exacerbation of the disease and significant extraskeletal morbidity and mortality. Thus, there is a need to identify more effective treatment approaches. This review discusses the pathophysiology of secondary HPT, the challenges faced in the management of this disorder, and the impact of current treatment options on patients’ risks of morbidity and mortality. In addition, the development of new, more physiologically relevant therapies, which may lead to successful management of secondary HPT, is reviewed.