The non-dioxin-like polychlorinated biphenyls (NDL-PCBs) constitute the major proportion of PCBs found in food and human tissues. It is important to improve our understanding of the toxicity, environmental and human risks associated with the NDL-PCBs, since their toxicology is incompletely characterized and a human health risk assessment is required. This paper discusses the selection of a training set of 20 tri- to hepta-chlorinated biphenyls, PCBs 19,28,47,51,52,53,74,95,100,101,104,118,122,128,136,138,153,170,180, and 190. Suggested for comprehensive screening using in vitro assays to identify critical mechanisms of toxicological action. The selected PCBs form a balanced basis for developing of quantitative structure-activity relationship (QSAR) models for prediction of physicochemical and toxicological properties of non-tested PCB congeners. Chemical and physical properties, environmental abundance and toxicological activities of the congeners were considered during the selection process. A complementary set of PCBs, a reference set, was selected using D-optimal onion design including PCBs 18,20,28,30,37,40,50,54,60,77,82,99,122,132,153,161,170,188,192, and 193. Congeners of this set are well suited for validation of QSAR models developed using the training set. For visualization of the chemical diversity of environmentally abundant PCBs and congeners of the training and reference sets, principal component analysis (PCA) was used. Statistical molecular design was used to verify the structural representation. As a reference structure for dioxin-like PCBs, PCB 126 was added in the training set. The selected set of NDL-PCBs is proposed for use in toxicological testing programs to provide rational basis for risk assessment of the NDL-PCBs.