Experimental approaches to the discovery of small molecule probes and drug candidates often use biochemical or cell-based screening of large libraries (>105) of small molecules. Small molecules of interest are tested one at a time in individual wells of a microtiter plate, at a significant cost in time and resources. Furthermore, evaluation of large numbers of compounds in such assays requires robust cellular or biochemical screening formats that may not be relevant to the contexts found in human patients. We envision a solution to these issues that involves a pooled system of small molecule screening, which would require development of numerous new technologies, and solutions to several key challenges. We report here that a microparticle-based screening system can allow for screening of small molecules in such a pooled fashion, analogous to the pooled screens of genetic reagents that have been powerfully deployed in recent years. We developed a cleavable linker that can link small molecules of interest to silica microparticle beads, a DNA tag encoding the identity of the small molecule on each bead that was attached to the silica beads through a photocleavable linker to enable its amplification, and a bead-based fluorescent sensor that can report on the activity of small molecules in cells. We suggest that this pooled small molecule screening system could ultimately be useful for drug and probe discovery, allowing rapid and inexpensive screening of small molecules in assays of relevance to human diseases.