A method and apparatus are provided for characterizing square wave jerks in the eye movements of a person, which may provide a powerful tool in the differential diagnosis of oculomotor and neurological disease. The method includes the steps of a) providing a sequence of saccades, b) identifying pairs of consecutive saccades of the sequence, c) determining whether each saccade of each identified pair is opposite the direction of the other saccade and, if not, then discarding the pair, d) determining whether a magnitude of each saccade of each identified pair is comparable and, if not, then discarding the pair, e) determining whether the pair of saccades of each identified pair are temporally related by a predetermined time period and, if not, then discarding the pair and f) collecting any remaining pairs of saccades as square wave jerks.