Protein-energy wasting (PEW) is one of the strongest risk factors of adverse outcomes in patients with chronic kidney disease including those with end-stage renal disease (ESRD) who undergo maintenance dialysis treatment. One important determinant of PEW in this patient population is an inadequate amount of protein and energy intake. Compounding the problem are the many qualitative nutritional deficiencies that arise because of the altered dietary habits of dialysis patients. Many of these alterations are iatrogenically induced, and albeit well intentioned, they could induce unintended harmful effects. In order to determine the best possible diet in ESRD patients, one must first understand the complex interplay between the quantity and quality of nutrient intake in these patients, and their impact on relevant clinical outcomes. We review available studies examining the association of nutritional intake with clinical outcomes in ESRD, stressing the complicated and often difficult-to-study inter-relationship between quantitative and qualitative aspects of nutrient intake in nutritional epidemiology. The currently recommended higher protein intake of 1.2 g/kg/day may be associated with a higher phosphorus and potassium burden and with worsening hyperphosphatemia and hyperkalemia, whereas dietary control of phosphorus and potassium by restricting protein intake may increase the risk of PEW. We assess the relevance of associative studies by examining the biologic plausibility of underlying mechanisms of action and emphasize areas in need of further research.