In this study, a unified framework to estimate different microstructure indices from diffusion MRI and multi-echo T2 (MET2) data was proposed.The new methodology takes into account the common and complementary information provided by both modalities. While the MET2 data enable us to model the myelin compartment, the diffusion data allow us to better characterize the intra-axonal and extra-axonal compartments. Numerical results support the hypothesis that the proposed approach is more accurate than the alternative approach based on the individual sequential fitting of both modalities. The performance was stable for noise levels commonly found in clinical protocols.