Multipotent mesenchymal stromal cells (MSC) are progenitor cells able to differentiate into several lineages including chondrocytes, and thus represent a suitable source of cells for cartilage engineering. However, the control of MSC differentiation to hypertrophy is a crucial step for the clinical application of MSC in cartilage repair where a stable chondrogenic phenotype without transition to terminal differentiation is the goal to achieve. This study aims at identifying new factors that may regulate this process. Using microarrays, we compared the transcriptional profiles of human MSC and MSC-derived chondrocytes obtained after culture in micropellets. After chondrogenesis induction, 676 genes were upregulated, among which five transcription factors not yet associated with chondrocyte differentiation of adult stem cells. These factors, in particular Foxo3A, are strongly expressed at day 21 and in mature chondrocytes. We investigated the role of Foxo3A using RNA interference. Our results revealed an important role of Foxo3A in the differentiation process of MSC toward chondrogenic fate, both in early and late stages. Indeed, stable Foxo3A knockdown tends to increase cell survival and decrease apoptosis, mainly in early stages of chondrogenesis. Importantly, we show that the loss of Foxo3A in MSC results in an increased expression level of markers specific for mature (aggrecan, collagen II) and hypertrophic (collagen X) chondrocytes. Therefore, our findings suggest that upregulation of Foxo3A over the course of chondrogenic differentiation plays a dual role, mainly inhibiting the differentiation process toward hypertrophy and promoting cell apoptosis.