Parathyroid hormone (PTH) and vitamin D [calcidiol or 25(OH)D] assays are used to diagnose chronic kidney disease-mineral bone disorder, and to guide and monitor interventions. Unfortunately, both assays have limitations. These limitations include analytical variability because of a lack of assay standardization, different calibrators used for each kit and differences in antibody specificity. For PTH assays, this leads to variability in the assessment of fragments and differences between results among kits from different manufacturers. For vitamin D, this leads to differences in the ability to detect D2 and D3 derivatives and differences among assays. For PTH, these problems are amplified by collection and handling differences and, for vitamin D, by diurnal and seasonal variation. Understanding these limitations should help clinicians to appropriately interpret results; attempts to develop universal standards to minimize these limitations may enhance the ability of these hormone measurements to predict underlying disease states.