High-throughput experimentation (HTE) is a well-established technique used in the pharmaceutical industry to accelerate compound synthesis and route optimization through automated chemical processes. A key part of any HTE workflow is the analytical component, through which the reaction outcome can be determined. The development of new analytical techniques capable of high-throughput data generation from nanoscale chemical reactions has been required to streamline the HTE process and address challenges generated through the recent move to miniaturize synthesis. In this Perspective, we review the currently available state-of-the-art analytical methods, discuss the challenges encountered in high-throughput analysiswith a particular focus on the analysis of nanoscale reactions, and provide a future outlook on potential developments in the field.