Chemicals may induce both numerical and structural aberrations. In addition to these chromosomal mutations, chemicals may render cells genetically unstable, which may result in chromosomal instability. For a detailed analysis, sophisticated approaches at single cell resolution are needed. Such approaches have become feasible by recent developments in molecular cytogenetics. In particular, new multicolor fluorescence in situ hybridization (FISH) technologies allow us now to study the effects of chemicals on chromosomes with unprecedented resolution. FISH provides opportunities to analyze the genome in two dimensions, i.e. on metaphase spreads, or in three dimensions, i.e. in interphase nuclei. An arsenal of diverse multicolor FISH approaches has been developed, which allows the analysis of the entire genome with one hybridization on metaphase spreads or the detailed visualization of selected chromosomal regions within intact interphase nuclei. These developments have been complemented by new resources for DNA probes, which have evolved from the human genome project. Here we will review the latest developments and provide some examples in which multicolor FISH technologies were applied to elucidate the effect of chemicals on chromosomes.