In a prospective study on latent autonomic dysfunction in the Chiari type I malformation, 15 patients were examined for degree of sinus arrhythmia in the supine and the sitting positions with a deep breathing test, and for pupil size and function with electronic pupillometry after sympathicomimetic eyedrop stimulation. The 5 patients with brainstem signs had a marked disturbance of sinus arrhythmia, which was more pronounced in the supine than in the sitting position. The clinical signs suggested a dysfunction of the reflex centers in the medulla rather than of the lower cranial nerves. The patients also tended to have more anisocoria than healthy controls, but no clear-cut pattern existed as to pupil dysfunction. Of the 4 patients with syringomyelia, however, the two with the most extensive cord cavitations had a Horner-like pupil reaction ipsilaterally to a marked hand wasting, indicating a sympathetic lesion at the T1 level of the cord.