Biomarkers that effectively document effects of chronic multi-generational exposure to contaminated environments on chromosomes would be valuable in risk assessment, remediation, and environmental decisions. Native, free-ranging populations of voles inhabiting the highly radioactive regions surrounding Reactor 4 of the Chornobyl Nuclear Power Station provide a model system to evaluate biological and chromosomal effects of chronic multi-generational exposure to radioactivity and other reactor meltdown-related pollutants. Here, we explore the utility of heterochromatic elements as potentially informative biomarkers for genetic damage in voles from the radioactive environments surrounding Chornobyl. We analyzed chromosomal positions of heterochromatin from Microtus arvalis and M. rossiaemeridionalis using fluorescent in situ hybridization. Although intrapopulational variation existed in chromosomal position and abundance of heterochromatin, none of that variation could be assigned to environmental exposure.