Manufacturing of autologous chondrocytes presents unique challenges, and robust and reliable release assays are required to ensure product quality. We have discovered markers that correctly identify chondrocytes and predict potency. Novel qPCR assays developed with these markers for our Matrix-induced Autologous Chondrocyte Implant product (MACI^® implant) are described. An identity assay must distinguish chondrocytes from potentially contaminating cell types, such as synovial fibroblasts. Microarray analysis of more than 47,000 transcripts led to the discovery of two markers, currently aliased “Cart1” and “Synov1”, that have been characterized as the two most differentially expressed mRNAs between chondrocyte and synovial fibroblast cultures. A potency assay must identify cells that have the potential to form hyaline-like cartilage. We examined expression of critical components of hyaline cartilage during the chondrocyte manufacturing process and in re-differentiation assays. From these studies a gene, which we call “Hyaline1”, was identified as a candidate potency marker. Using an assay measuring the ratio of Cart1:Synov1, a large population study of chondrocyte and synovial fibroblast cultures examined the assay’s suitability for identity classification with our proposed Cart1:Synov1 acceptance boundary. In this study, assay specificity and sensitivity were both observed to be 100%. The utility of the assay was further demonstrated in mixing experiments, where a majority of chondrocytes (in mixtures with synovial fibroblasts) was required to pass the assay acceptance. These results indicate that the assay is useful for determination of both culture identity and culture homogeneity, and thus represents a significant improvement over previous identity assays. The potency assay is also a real-time quantitative RT-PCR assay that measures levels of Hyaline1. Characterization of MACI^® implants indicated that Hyaline1 is stable in long-term culture of chondrocytes but not fibroblasts on ACI-Maix membrane, and is overexpressed in chondrocytes compared fibroblasts that had been recovered from MACI^® implants and tested in various redifferentiation assays. These data suggest that Hyaline1 is predictive of the chondrogenic potential of cells used to manufacture MACI^® implants. After comparing may cell strains, a threshold level which indicates product potency was established. The identification of genetic markers that unambiguously identify cultured chondrocytes has been a long-standing challenge. Another challenge has been the ability to predict re-differentiation capacity of cultured chondrocytes. Modern techniques like whole genome microarray analysis have enabled us to develop novel identity and potency assays for quality control of MACI^® implants.