In this pilot study we investigated the hypothesis that intrinsic and extrinsic brainstem lesions situated within the pontomedullary region would effect the integrity of respiratory sinus arrhythmia. The study sample consisted of three patients with anatomic brainstem abnormalities associated with isolated Chiari I malformation, Chiari II malformation with syringobulbia, and achondroplasia with cervicomedullary compression. They were compared to an age- and sex-matched control group of nine patients. Each subject's electrocardiogram was recorded in a quiet room and digitized by a personal computer during five 1-minute periods. R-R intervals within each 1-minute period were converted to heart rate in 120 successive 0.5-second intervals. The resultant heartrate time series was converted to its underlying frequency composition by a fast Fourier transform and averaged across minutes. Respiratory sinus arrhythmia was defined as the variability in the time series over a frequency range (0.096 to 0.48 Hz) corresponding to a range of respiratory rates from 6 to 30 breaths per minute. Analysis revealed a significant reduction in respiratory sinus arrhythmia (P < .05), defined as the summated area under the curve, with a mean for controls of 35.42+/-28.13 SD and for subjects of 17.20+/-11.50 SD. There was a gradient of abnormality noted, with the mildest deviation in respiratory sinus arrhythmia for the patient with isolated Chiari I malformation and maximum deviation seen in the patient with extrinsic cervicomedullary compression.