Big data trends in biomedical and health research enable large-scale and multi-dimensional aggregation and analysis of heterogeneous data sources, which could ultimately result in preventive, diagnostic and therapeutic benefit. The methodological novelty and computational complexity of big data health research raises novel challenges for ethics review. In this study, we conducted a scoping review of the literature using five databases to identify and map the major challenges of health-related big data for Ethics Review Committees (ERCs) or analogous institutional review boards. A total of 1093 publications were initially identified, 263 of which were included in the final synthesis after abstract and full-text screening performed independently by two researchers. Both a descriptive numerical summary and a thematic analysis were performed on the full-texts of all articles included in the synthesis. Our findings suggest that while big data trends in biomedicine hold the potential for advancing clinical research, improving prevention and optimizing healthcare delivery, yet several epistemic, scientific and normative challenges need careful consideration. These challenges have relevance for both the composition of ERCs and the evaluation criteria that should be employed by ERC members when assessing the methodological and ethical viability of health-related big data studies. Based on this analysis, we provide some preliminary recommendations on how ERCs could adaptively respond to those challenges. This exploration is designed to synthesize useful information for researchers, ERCs and relevant institutional bodies involved in the conduction and/or assessment of health-related big data research.