Human embryonic stem cells (hESCs) are pluripotent and, thus, have enormous potential as therapeutic cells in regenerative medicine. Non-invasive tracking of transplanted cells is critical for advancing cell-based therapies. MRI has emerged as an important technique for monitoring the fate of transplanted cells. However, conventional cellular MRI uses superparamagnetic iron oxide nanoparticles (SPIOs) that have limited specificity. To improve specificity, we developed a highly efficient, cell-permeable T1 agent for labeling hESCs without affecting cell viability, proliferation, or function. MR imaging of transplanted hESCs demonstrates sensitive detection of labeled cells in vivo.