Organic cation transporters (OCTs) 1, 2, and 3 facilitate cellular uptake of structurally diverse endogenous and exogenous substances. However, their substrate and inhibitor specificity are not fully understood. We performed a broad in vitro screening for OCT3 substrates and inhibitors, allowing us to compare the substrate spectra and to study the relationship between transport and inhibition of transport. Generally, substrates were smaller and more hydrophilic than OCT3 inhibitors. The best model-based predictor of transport was the positive charge, while the best predictor of inhibition was the aromatic ring count. OCT3 inhibition was well correlated between different model substrates. Substrates of OCT3 were mainly weak inhibitors, and the best inhibitors were not substrates. As tested with 264 substances, OCT3 transport had significantly more overlap with OCT2 than OCT1. Our data further substantiate that specificity of OCT transport varies with minor substitutions rather than with the general scaffolds of substrates.