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The clinical laboratory plays a critical role in healthcare delivery by providing objective data on specific biomarkers that directly aid in the diagnosis and monitoring of a wide range of clinical disorders. Reliable and accurate reference intervals for laboratory analyses are integral for correct interpretation of clinical laboratory test results and, therefore, for appropriate clinical decision-making. Ideally, reference intervals should be established based on a healthy population and stratified for key covariates including age, gender and ethnicity. However, establishing reference intervals can be challenging as it requires the collection of large numbers of samples from healthy individuals. This challenge is further augmented in pediatrics, where dynamic changes due to child growth and development markedly affect circulating levels of disease biomarkers. As a result, even larger reference populations are required to reliably calculate reference intervals. In this review, we outline the challenges specific to establishing pediatric reference intervals and highlight recent initiatives aimed at closing existing gaps in current knowledge. We also outline recommended approaches to the development of reference intervals and detail several alternative approaches. Finally, reference intervals for emerging and novel biomarkers of pediatric disease are discussed along with a number of potential alternative sample types.