Epidemiology is struggling increasingly with problems with correlated exposures and small relative risks. As a consequence, some scholars have strongly emphasized molecular epidemiology, whereas others have argued for the importance of the population context and the reintegration of epidemiology into public health. Environmental epidemiology has several unique features that make these debates especially pertinent to it. The very large number of environmental exposures require prioritization, and the relative risks are usually very low. Furthermore, many environmental exposures can be addressed only by comparing populations rather than individuals, and the disruption of both local and global ecosystems requires us to develop new methods of study design. The population context is also very important to consider in risk management decisions because of the involuntary nature of most environmental exposures and the diversity of possible outcomes, both health- and nonhealth-related. Studies at the individual or molecular level tend to focus the research hypotheses and subsequent interventions at that level, even when research and interventions at other levels may be more appropriate. Thus, only by starting from the population and ecosystem levels can we ensure that these are given appropriate consideration. Although better research is needed at all levels, it is crucially important to choose the most appropriate level, or levels, of research for a particular problem. Only by conducting research at all these levels and by developing further methods to combine evidence from these different levels can we hope to address the challenges facing environmental epidemiology today.