Analyzing the integrity of DNA is one of the most frequent used endpoints for risk assessment of chemical and physical agents. In the framework of a radiobiological space experiment, this work aimed at having (1) a histochemical tool for the in situ assessment of DNA damage in as long as 20 days old fixed cell cultures, (2) a comprehensive tool for the quantification of different types of DNA lesions, and (3) a methodology of sampling thousands of nuclei based on confocal microscopy, automated stage scanning and digital image processing. For this purpose several fixatives and permeabilization techniques were tested together with the combinatorial use of terminal dUTP transferase-mediated nick end-labeling (TUNEL) and the DNA polymerase I mediated in situ nick translation. These biochemical tools are useful for scoring DNA single and double breaks, and oxidative lesions. Ltk(-) cells were exposed either to hydrogen peroxide or heavy ion beam irradiation. Combination of paraformaldehyde fixation, sodium citrate permeabilization and heat gave the best staining results. A three-channel fluorescence methodology was established including a DNA counter stain for nucleus identification and normalization of DNA content. Communication between confocal imaging software, image analysis software and a relational database proved to be pivotal for a semi-automated high-end single cell analysis and storage of images. In this way, DNA damage data per nucleus can be traced back to the original image. As much as 2500 cells could be analyzed in situ within a day and correlations drawn between different DNA lesion endpoints.