Anaesthesia and minor surgery to place electrocardiogram recording electrodes in the short-horned sculpin caused a decrease in mean normal beat (R-R) interval and heart rate variability (HRV), measured as the standard deviation in the R-R interval (SDRR). Mean R-R interval increased to a steady state value (1.9+/-2.9 s) 72 h post-surgery, but SDRR took 120 h to stabilise (0.56+/-0.09 s). Power spectral analysis applied to recordings of instantaneous heart rate showed no spectral peaks immediately after surgery, with the development of twin peaks (at 0.02 and 0.05 Hz) that also became stable 120 h post surgery. Bilateral cardiac vagotomy abolished the variability in beat-to-beat interval, and both the high and low frequency peaks, suggesting that much of the regulation of heart rate and HRV in sculpin was under parasympathetic, cholinergic control that was withdrawn as a result of surgical and handling stress. Rate of oxygen consumption and heart rate (f(H)) were monitored simultaneously and showed a good correlation with both mean R-R interval (r(2)=-0.89) and SDRR (r(2)=0.93), although a more significant (ANCOVA, P=0.02) covariance existed between the post-surgical decrease in and increase in SDRR. These data suggest that sculpin use f(H) as a way of moderating oxygen consumption, fine-tuned on a beat-to-beat basis by cholinergic control. We conclude that power spectral analysis is a useful method of determining HRV in fish, and that HRV is a more sensitive measure of recovery from disturbance than f(H) alone.