Ultra-high field magnetic resonance imaging data obtained using a multi-echo gradient echo sequence has been shown to contain information on tissue microstructure. Quantitative assessment of water fraction, relaxation time and frequency shift using multi-compartment signal modelling may help improve our understanding of diseases and disorders affecting the human brain. In this study, we explored tissue microstructure information by analysing voxel compartment water fraction and frequency shifts derived from 7 T multi-echo gradient recalled echo MRI data. We aimed to test whether the parameters of a three compartment model could distinguish the normal cortex from the cortex affected by focal cortical dysplasia. We compartmentalised normal and dysplastic cortical regions in patients diagnosed with focal cortical dysplasia. We found the frequency shift parameter of the shortest T2⁎ signal compartment to be sensitive to regions of dysplastic tissue. We conclude that mathematical modelling of echo time dependent gradient recalled echo MRI signals in patients with focal cortical dysplasia can potentially delineate cortical areas that have undergone microstructural changes in comparison to normal tissue.