This paper presents the preparation, characterisation and validation of two quality control (QC) samples for the measurement of plutonium and uranium contents by isotope dilution mass spectrometry (IDMS). These two QC samples were then used at the JRC-Geel G.2′s laboratory to monitor the performance of IDMS measurement results in line with the ISO 17025 and ISO 17034. The QC samples were prepared from two certified reference materials, namely the NBL-126 (Pu) and CRM 116-A (U). The values for the 235U and 239Pu amount contents of the QC samples were assigned based on the gravimetric preparation of the solutions and verified by independent IDMS measurements. Their use as part of a broader in-house spike inter-calibration campaign, notably during participations in proficiency tests, is also highlighted. Finally, using these two IDMS QC samples, a detailed approach to the IDMS uncertainty evaluation, according to the Guide to the expression of uncertainty in measurement (GUM, 2008) is presented on various examples.