High throughput screening has emerged as a powerful technique for discovering novel medical tools and therapies. This is particularly true for biomaterials that are applied to poorly understood biological-material systems. The polymer microarray format has become a key enabling tool for high throughput materials discovery, whereby hundreds to thousands of unique polymers can be presented on a single glass slide and screened in parallel for biological interactions of interest. This approach has successfully been utilized to develop the surface chemistry, topography, bioactivity, and mechanical properties of biomaterials as well as allowing the development of 3D culture systems. In order to optimize a polymer microarray for a given application the substrate used, the coating on the substrate, and the material library screened must be carefully selected. Furthermore, development of suitable biological assays with high throughput readouts is imperative for expanding the applications of polymer microarrays. The biological systems screened on this format include supporting cell attachment and outgrowth, maturation and phagocytosis of dendritic cells, materials resistant to microbes, switchable materials, platelet activation, cell sorting, hepatocytes and toxicity models, and cell transfection. Further to the discovery and development of biomaterials, the large datasets when coupled with modelling techniques can establish structure-function relationships that help elucidate the underlying biological-material interactions. Continued development of microarray designs and high throughput biological assays compatible with the format will lead to the discovery of new biomaterials that exhibit unprecedented control over the biological systems they are designed to function in.