In this work, a practical approach to assessing bias and uncertainty using patient samples in a clinical laboratory is presented. The scheme is essentially a splitsample setup where one instrument is appointed to being the “master” instrument which other instruments are compared to. The software presented automatically collects test results from a Laboratory Information System in production and couples together the results of pairwise measurements. Partitioning of measurement results by user-defined criteria and how this can facilitate isolation of variation sources are also discussed. The logic and essential data model are described and the surrounding workflows outlined. The described software and workflow are currently in considerable practical use in several Swedish large-scale distributed laboratory organizations. With the appropriate IT-support, split-sample testing can be a powerful complement to external quality assurance.