Environmental factors such as chemical exposures are likely to play a crucial role in the development of several human chronic diseases. However, how the specific exposures contribute to the onset and progress of various diseases is still poorly understood. In part, this is because comprehensive characterization of the chemical exposome is a highly challenging task, both due to its complex dynamic nature as well as due to the analytical challenges. Herein, the analytical challenges in the field of exposome research are reviewed, with specific emphasis on the sampling, sample preparation and analysis, as well as challenges in the compound identification. The primary focus is on the human chemical exposome, i.e., exposures to mixtures of environmental chemicals and its impact on human metabolome. In order to highlight the recent progress in the exposome research in relation to human health and disease, selected examples of human exposome studies are presented.