Biomarkers of nutritional status provide alternative measures of dietary intake. Like the error and variation associated with dietary intake measures, the magnitude and impact of both biological (preanalytical) and laboratory (analytical) variability need to be considered when one is using biomarkers. When choosing a biomarker, it is important to understand how it relates to nutritional intake and the specific time frame of exposure it reflects as well as how it is affected by sampling and laboratory procedures. Biological sources of variation that arise from genetic and disease states of an individual affect biomarkers, but they are also affected by nonbiological sources of variation arising from specimen collection and storage, seasonality, time of day, contamination, stability and laboratory quality assurance. When choosing a laboratory for biomarker assessment, researchers should try to make sure random and systematic error is minimized by inclusion of certain techniques such as blinding of laboratory staff to disease status and including external pooled standards to which laboratory staff are blinded. In addition analytic quality control should be ensured by use of internal standards or certified materials over the entire range of possible values to control method accuracy. One must consider the effect of random laboratory error on measurement precision and also understand the method's limit of detection and the laboratory cutpoints. Choosing appropriate cutpoints and reducing error is extremely important in nutritional epidemiology where weak associations are frequent. As part of this review, serum lipids are included as an example of a biomarker whereby collaborative efforts have been put forth to both understand biological sources of variation and standardize laboratory results.