Non-invasive mapping of cell size distribution provides a unique means to probe biological tissues. We introduce a diffusion MRI based framework that does not require prior assumptions on distribution functions to provide tissue microstructural properties including non-cell-volume-weighted cell size distributions. We validated this approach, which we call MRI-cytometry, comprehensively using computer simulations in silico, cultured cells in vitro, and animal xenografts in vivo. We then demonstrate the implementation of MRI-cytometry in imaging breast cancer patients using clinical 3T MRI, indicating its potential clinical application such as more specific assessments of tumor status and therapeutic responses.