Studying cell behavior within 3D material niches is key to understanding cell biology in health and disease, and developing biomaterials for regenerative medicine applications. Current approaches to study these cell-material niches are low throughput and can only analyze few replicates per experiment resulting in reduced measurement assurance and analytical power. Here we report 3D Material Cytometry (3DMaC), a novel high-throughput method based on microfabricated, shape-specific 3D cell-material niches and imaging cytometry. 3DMaC achieves rapid and highly multiplexed analyses of very high replicate numbers (“n” of 104-106) of 3D biomaterial constructs. 3DMaC overcomes current limitations of low “n”, low-throughput, “noisy” assays, to provide rapid, simultaneous analyses of potentially hundreds of parameters in 3D biomaterial cultures. The method is demonstrated here for a set of 85,000 events containing twelve distinct cell-biomaterial micro-niches along with robust, customized computational methods for high-throughput analytics with potentially unprecedented statistical power.