We report a novel and simple application of skin conductance response (SCR) testing for diagnosis of a new-onset iatrogenic Harlequin syndrome in an infant. Isolated ipsilateral facial pallor, complicated by thermally induced systemic sympathetic vasodilatation, and preferential lateral decubitus positioning, mimics harlequin colour change. Correct diagnosis as Harlequin syndrome with facial sympathetic interruption was demonstrated by diminution of SCR.