Polybrominated diphenyl ethers (PBDE) exposures affect epigenetic regulatory mechanisms at multiple levels, across multiple biological systems. There are several major aspects of human health that are of concern regarding PBDE toxicity that now have evidence for an involvement of dysregulated epigenetic regulation. These include: nervous system toxicity, disruption of thyroid hormone signaling, effects on the reproductive system (primarily on the placenta and testes), and oncogenic potential. One or more epigenetic components are known to be disrupted in each of these systems. In this review, we discuss these epigenetic regulators, their known modes of disruption by PBDEs, and the relationship of these disruptions to human health.