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In eukaryotes, the packaging of DNA into nucleosomes and the organization of chromatin fibres generate constraints for all nuclear processes involving DNA, including replication, repair, recombination and transcription. The three major processes that regulate chromatin structure and counterbalance its repressive effects are ATP-dependent chromatin remodeling, post-translational modification of histones and histone replacement. While many of these processes have been intensively studied with respect to their effects on transcription, there is also evidence that they affect other nuclear processes involving DNA. This review explores the functions of chromatin-remodeling factors and histone-modifying enzymes in gene regulation and summarizes recent findings which suggest a role for these chromatin modifiers in DNA repair.