The aim of the 'BioQuaRT' (Biologically weighted Quantities in RadioTherapy) project is to develop measurement techniques for characterising charged particle track structure on different length scales, and to correlate at the cellular level the track structure properties with the biological effects of radiation. This multi-scale approach will allow characterisation of the radiation qualities used in radiotherapy and the related biological effects. Charged-particle microbeam facilities were chosen as the platforms for all radiobiology experiments in the 'BioQuaRT' project, because they allow targeting single cells (or compartments of a cell) with a predefined number of ionising particles and correlating the cell-by-cell induced damage with type and energy of the radiation and with the number of ions per cell. Within this project, a novel in situ protocol was developed for the analysis of the misrepaired and/or unrepaired chromosome damage induced by charged-particle irradiations at the Physikalisch-Technische Bundesanstalt (PTB) ion microbeam facility. Among the cytogenetic biomarkers to detect and estimate radiation-induced DNA damage in radiobiology, chromosomal aberrations and micronuclei were chosen. The characteristics of the PTB irradiation system required the design of a special in situ assay: specific irradiation dishes with a base made from a biofoil 25-μm thick and only 3000-4000 cells seeded and irradiated per dish. This method was developed on Chinese hamster ovary (CHO) cells, one of the most commonly used cell lines in radiobiology in vitro experiments. The present protocol allows the simultaneous scoring of chromosome aberrations and micronuclei on the same irradiated dish. Thanks to its versatility, this method could also be extended to other radiobiological applications besides the single-ion microbeam irradiations. © The Author 2015.