The sympathetic nervous system dominates the regulation of body functions during exercise. Therefore after exercise, the sympathetic nervous system withdraws and the parasympathetic nervous system helps the body return to a resting state. In the examination of this relationship, the purpose of this study was to compare recovery heart rates (HR) of anaerobically versus aerobically trained cyclists. With all values given as means ± SD, anaerobically trained track cyclists (n=10, age=25.9 ± 6.0 yrs, body mass=82.7 ± 7.1 kg, body fat=10.0 ± 6.3%) and aerobically trained road cyclists (n=15, age=39.9 ± 8.5 yrs, body mass=75.3 ± 9.9 kg, body fat=13.1 ± 4.5%) underwent a maximal oxygen uptake test. Heart rate recovery was examined on a relative basis using heart rate reserve as well as the absolute difference between maximum HR and each of two recovery HRs. The post-exercise change in HR at minute one for the track cyclists and road cyclists respectively were 22 ± 8 bpm and 25 ± 12 bpm. At minute two, the mean drop for track cyclists was significantly (p<0.05) greater than the road cyclists (52 ± 15 bpm and 64 ± 11 bpm). Training mode showed statistically significant effects on the speed of heart rate recovery in trained cyclists. Greater variability in recovery heart rate at minute two versus minute one suggests that the heart rate should be monitored longer than one minute of recovery for a better analysis of post-exercise autonomic shift.