Axonal loss within chronic MS lesions is typically accompanied by increase of extra-cellular space. Reduction of anisotropy caused by this excessive extra-cellular water may limit the ability of tractography techniques to accurately detect fibre bundles. The aim of this study was to examine if application of free water elimination (FWE) algorithm may improve deterministic tractography through MS lesions. We show that elimination of free water markedly increases detection of lesional fibre bundles. While this effect was observed in the majority of lesions, it was more apparent in lesions with small initial number of fibres and in lesions categorised as severely damaged.