In conventional intravoxel incoherent motion (IVIM) imaging, the blood fraction is estimated using a two-compartment model (blood and tissue). However, blood fraction estimation is hampered by cerebrospinal fluid (CSF) contamination and tissue-dependent relaxation times. We propose a three-compartment model (blood, tissue, CSF), which accounts for compartment-specific diffusion and relaxation properties. Estimation of gray and white matter blood fractions using this model is demonstrated with in-vivo human data of variable diffusion weightings, echo times and inversion times. In comparison with two-compartment models (with and without relaxation), the proposed three-compartment model yielded lower estimates of the blood fraction, suggesting a better separation from CSF.