Purpose: To standardise the scan protocol for CT scanners of participating centres in a multi-centre study (clinicaltrials.gov NCT01270074) for the prevention of radiologically defined bronchiectasis in CF infants by ensuring the maximum image quality at the minimum radiation dose. Methods and Materials: Three different sized phantoms (QRM, Germany) were used to assess scanners’ performance of automatic exposure control (AEC). CTDI and DLP were recorded. The phantoms contained various inserts to assess slice-sensitivity-profile, in-plane spatial resolution, noise and the Hounsfield Unit (HU) scale. Scans were made for several dose levels and reconstruction kernels. Images were analysed with custom-made software (MatLab, USA) to obtain the standard deviation of the noise, point-spread-function (PSF) and slice thickness. Results: Eight different scanners with 64 slices or more from 4 manufacturers (GE, Philips, Siemens and Toshiba) were assessed. Despite differences in AEC’s performance, we obtained approximately the same dose level at each center by recommending site and age-specific AEC reference levels. A constant image quality was only possible by matching the different reconstruction kernels measured PSFs at full-width-at-half-maximum. In fact, large part of the differences between scanners was related to reconstruction kernels. The relatively high noise images corresponded with reconstructions using a kernel with edge enhancement such as the Siemens B70 kernel or the GE lung kernel that are routinely used in chest imaging. Conclusion: Objective measurements on CT images allowed for matching of scan protocols among CT scanners of different manufacturers. Use of routine protocols might introduce a bias in the (automated) image analysis.