Processing of DNA lesions by structure-specific nucleases results in DNA–protein intermediates, which form the basis for checkpoint activation and DNA repair. Post-translational modifications like phosphorylation and ubiquitination modulate the DNA damage response in a spatial and temporal manner. Cell cycle-dependent regulation additionally plays a key role in the regulation of both DNA repair and checkpoint activation. We highlight recent advances in in vivo imaging that greatly expand our knowledge on the relationships between DNA damage checkpoints and DNA repair.