Historically, traditional screening for ligands has been optimized to detect standard orthosteric agonists and antagonists. However, with increasing emphasis on cellular functional screens, more allosteric ligands are being discovered as potential drugs. In addition, there are theoretical reasons (increased selectivity, better control of physiological systems, separate control of affinity and efficacy) allosteric ligands may be preferred therapeutic chemical targets. These factors may make it desirable to design high-throughput screens to specifically detect functionally allosteric ligands. This article discusses the unique features of allosteric ligands as drugs as well as the special conditions that should be considered to optimize a high-throughput screen toward the detection of allosteric drugs. Finally, the likelihood of detecting allosteric ligands that have direct effects on cells (either conventional agonism or functionally selective effects) is discussed as well as the optimization of detection of such ligands in screening assays.