Mesenchymal stem cells (MSCs) are a multi-potential cell type that can be induced to differentiate to a variety of tissue-specific cell phenotypes, including cartilage (chondrogenesis) and bone (osteogenesis). Given this multi-potentiality, MSCs are a promising cell source for exploring developmental paradigms and for tissue engineering (TE) applications. For cartilage formation assays, MSCs are collected in high-density pellets and treated with specific biofactors, including TGF-β superfamily members and dexamethasone in a chemically defined medium (CM) [1]. During chondrogenesis, extracellular matrix (ECM) rich in glycosaminoglycan (GAG) and type II collagen is synthesized. While MSC chondrogenesis is well-characterized using existing protocols, the effect of alternative biofactors, their doses and combinations requires laborious combinatorial studies [2]. High-throughput screening (HTS) overcomes this limitation through the simultaneous layout and query of a large number of conditions within a single plate. HTS depends on the use of precise robotic liquid handling systems and on the development of sensitive, validated, and readily quantifiable assays. In a recent study, we optimized cell culture and assay procedures for HTS by minimizing cell number, handling and culture duration [3]. We successfully reduced the time scale from 21 to 7 days and the number of cells required from 225K to 30K cells per pellet. Further, we developed a novel in-well digestion protocol to enable high-throughput analysis and minimize handling. In this study, we have further streamlined these assays for HTS by providing a rapid and robotic approach for layout, culture, and analysis of ECM deposition using ‘micro’ MSC pellets (10K cells per pellet) in a 384-well format. Furthermore, we have carried out an initial screen of the NINDS small molecule library and demonstrated the feasibility of this technology for use in HTS of chondrogenesis.