Unilateral elbow pain results in sensori-motor dysfunction that is frequently bilateral, affects local and remote upper limb muscles and persists beyond resolution of local tendon symptoms. These characteristics suggest supraspinal involvement. Here we investigated i) the excitability and organisation of the M1 representation of the wrist extensor muscles and ii) the relationship between M1 changes and clinical outcomes in lateral epicondylalgia (LE; n= 11) and healthy control subjects (n= 11). Transcranial magnetic stimulation was used to map the M1 representation of extensor carpi radialis brevis (ECRB) and extensor digitorum (ED). The cortical representations of ECRB and ED were more excitable and the centres of gravity (CoG) for the two muscles were located closer together in LE than healthy controls. Increased ECRB excitability and closer location of the CoG were associated with higher pain severity at rest and/or in the preceding 6 months. A novel finding was a reduced number of discrete peaks in the representations of ECRB and ED in LE compared with healthy controls. This finding may have broad implications for control of the wrist extensor muscles in LE. These data provide evidence that cortical organisation may be maladaptive in LE and suggest that reorganisation may be associated with persistence/recurrence of pain.