We present the use of two-photon excited fluorescence (TPEF) as a noninvasive means to monitor differentiation of human mesenchymal stem cells (hMSCs) into an adipogenic pathway relying entirely on endogenous sources of contrast. Specifically, we demonstrate that TPEF can be used to reveal quantitative differences in the biochemical status and the shape of differentiating and nondifferentiating stem cells in two-dimensional (2-D) cultures. We find that even in simple 2-D cultures, not all cells are undergoing differentiation at the same rate. Last, such noninvasive approaches may also ultimately allow for determination of the lineage toward which the cells are differentiating (e.g., fat versus bone). Thus, intrinsic TPEF imaging provides quantitative morphological and biochemical biomarkers associated with stem cell differentiation and could serve as an important enabling technology in tissue engineering applications.