AbstractThis report provides guidance for users of linear accelerator (linac) manufacturer integrated quality control (MIQC) tools. MIQC tools have been developed and introduced by radiotherapy linac vendors, and have the potential to improve both the quality and efficiency of linac quality control (QC). They usually utilise the Electronic Portal Imaging Device (EPID), but may acquire data from other sources, and automatically perform and analyse tests of various treatment machine QC parameters. The currently available systems meeting this definition are Varian machine performance check, CyberKnife automated quality assurance /end-to-end, TomoTherapy Quality Assurance, and Elekta machine QA (also known as AQUA). This guidance report covers the commissioning and implementation of MIQC. The guidance has been developed by a radiotherapy special interest group working party on behalf of the Institute of Physics and Engineering in Medicine. Recommendations within the report are derived from the experience of the working party members, existing guidance, literature, and a United Kingdom survey conducted in 2022 (Pearson et al 2023 Phys. Med. Biol.68 245018). Topics covered include developing an understanding of the QC system, independence review of MIQC, commissioning, implementation, ongoing QC and calibration, software upgrades and periodic review. The commissioning section covers detector commissioning, repeatability and reproducibility, baseline and tolerance setting, concordance with existing QC, sensitivity testing, cost-benefits analysis, and risk assessment methods. In order to offer practical guidance, case studies covering each aspect of commissioning are included. They are real-world examples or experiences from early adopters, each applied to a different example MIQC system. The examples will be directly applicable to users of that specific MIQC system, but also provide practical guidance on clinical implementation to users of the other systems.