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Engineered nanomaterials (ENMs) raise questions among the scientific community and public health authorities about their potential risks to human health. Studying a prospective cohort of workers exposed to ENMs would be considered the gold standard for identifying potential health effects of nanotechnology and confirming the ‘no effect’ levels derived from cellular and animal models. However, because only small, cross-sectional studies have been conducted in the past 5 years, questions remain about the health risks of ENMs. This essay addresses the scientific, methodological, political and regulatory issues that make epidemiological research in nanotechnology-exposed communities particularly complex. Scientific challenges include the array of physicochemical parameters and ENM production conditions, the lack of universally accepted definitions of ENMs and nanotechnology workers, and the lack of information about modes of action, target organs and likely dose–response functions of ENMs. Standardisation of data collection and harmonisation of research protocols are needed to eliminate misclassification of exposures and health effects. Forming ENM worker cohorts from a combination of smaller cohorts and overcoming selection bias are also challenges. National or international registries for monitoring the exposures and health of ENM workers would be helpful for epidemiological studies, but the creation of such a registry and ENM worker cohorts will require political support and dedicated funding at the national and international levels. Public authorities and health agencies should consider carrying out an ENM awareness campaign to educate and engage all stakeholders and concerned communities in discussion of such a project.