The neural substrate of estimating short temporal intervals is still unknown. We investigated the ability of patients with infarctions of the middle cerebral artery of either the left or the right hemisphere to estimate verbally and produce time intervals of seconds by counting. Patients showed long-lasting and stable deficits in time estimation in both methods, with either extreme acceleration or deceleration in apparent time compared with healthy controls. A lesion of the posterior part of the supralenticular white matter proved to be responsible for these deficits. Disruption of interneuronal communication therefore leads to a lasting alteration of a learned time-pacing synchronized to conventional time units.