Body integrity dysphoria (BID) is a severe condition affecting non-psychotic individuals where a limb may be experienced as non-belonging, despite normal anatomical development and intact sensorimotor functions. Limb amputation is desired for restoring their own identity. We previously demonstrated altered brain structural (gray matter) and functional connectivity in 16 men with a long-lasting and exclusive desire for left leg amputation. Here we aimed to identify in the same sample altered patterns of white matter structural connectivity. Fractional anisotropy (FA), derived from Diffusion Tensor Imaging data, was considered as a measure of structural connectivity. Results showed reduced structural connectivity of: i) the right superior parietal lobule (rSPL) with the right cuneus, superior occipital and posterior cingulate gyri, and cuneus, ii) the pars orbitalis of the right middle frontal gyrus (rMFGOrb) with the putamen iii) the left middle temporal gyrus (lMTG) with the pars triangularis of the left inferior frontal gyrus. Increased connectivity was observed between the right paracentral lobule (rPLC) and the right caudate nucleus. By using a complementary method of investigation, we confirmed and extended previous results showing alterations in areas tuned to the processing of the sensorimotor representations of the affected leg (rPCL), and to higher-order components of bodily representation such as the body image (rSPL). Alongside this network for bodily awareness, other networks such as the limbic (rMFGOrb) and the mirror (lMTG) systems showed structural alterations as well. These findings consolidate current understanding of the neural correlates of BID, which might in turn guide diagnostics and rehabilitative treatments.