Heart rate variability is an established risk factor for mortality in both healthy dogs and animals with heart failure. The aim of this study was to compare short-term heart rate variability (ST-HRV) parameters from 60-min electrocardiograms in dogs with sick sinus syndrome (SSS, n=20) or chronic mitral valve disease (CMVD, n=20) and healthy controls (n=50), and to verify the clinical application of ST-HRV analysis. The study groups differed significantly in terms of both time - and frequency- domain ST-HRV parameters. In the case of dogs with SSS and healthy controls, particularly evident differences pertained to HRV parameters linked directly to the variability of R-R intervals. Lower values of standard deviation of all R-R intervals (SDNN), standard deviation of the averaged R-R intervals for all 5-min segments (SDANN), mean of the standard deviations of all R-R intervals for all 5-min segments (SDNNI) and percentage of successive R-R intervals >50 ms (pNN50) corresponded to a decrease in parasympathetic regulation of heart rate in dogs with CMVD. These findings imply that ST-HRV may be useful for the identification of dogs with SSS and for detection of dysautonomia in animals with CMVD.