Hand nerve transection injuries precipitate a variety of reorganisational changes in both the peripheral and central nervous systems. Surgical repair restores the continuity of severed nerves, yet regenerating fibres establish new connections without topographical guidance, rearranging the branching architecture of peripheral nerves in the hand. In non-human primates, forelimb nerve transection and repair dramatically alters the otherwise orderly and highly conserved organisation of the digit maps in primary somatosensory areas 3b and 1. Digit-map organisation becomes patchwork and highly variable. Although without compelling evidence, these same reorganisational changes are presumed to occur in humans and to have significant functional implications for patient recovery. In the current study, we evaluate these assumptions. Functional MRI is used to characterise the fine-grained organisation of digit responses in the primary somatosensory cortex in twenty-one patients with nerve transection injuries and thirty healthy controls. Both univariate dice overlap coefficients and state-of-the-art multivariate representational distances are used to quantify the extent and pattern of interdigit response separability in primary somatosensory cortex. Our results reveal significant differences between patients and controls. The fine-grained organisation of the primary somatosensory cortex is altered in nerve repair. Average dice coefficients reveal significantly increased interdigit response overlap. These effects are specific to the hemisphere contralateral to the nerve-repaired hand, reflecting inputs from reinnervated digits, and are more robust within the cortical zones of the repaired nerves. Nerve repair also alters the relative functional structure of the primary somatosensory cortex, changing the otherwise stereotypical pattern of interdigit response separability seen in healthy controls. Unexpectedly, these later alterations manifest bilaterally, as maps for the healthy hand of patients also show an atypical pattern of interdigit response separability. Our findings provide the first compelling evidence for altered digit maps following nerve repair in humans, bridging results from animal models. Nonetheless, the clinical significance of the changes we observe remains unclear. No reliable relationships between fMRI measures of cortical reorganisation and behavioural measures of functional impairments are observed. Altered digit maps are not found to correlate with impairments in touch localisation or with broader measures of functional impairment as captured by sensory Rosen scores.