Modulators of ligand gated ion channel (LGIC) activity are being actively developed by a number of leading pharmaceutical companies. Electro- physiology assays remain the gold standard for determining functional compound effects on these targets, and pose unique challenges due to the need for accurate temporal control of agonist and compound applica- tion. In this study we present results from complex assays enabled by a novel microfluidic automated patch clamp platform. The data includes case studies from NMDA receptors, nicotinic receptors and GABA recep- tors and trade-offs between the different available measurement modali- ties developed. For targets where cell byproducts activate the channel (such as NMDA) continuous perfusion is required for removing such products from the extracellular space in order to obtain a robust assay. Continuous perfusion is also essential for accurate measurements of channel recovery times are important (nicotinic receptors).