Graphical plots of beat-by-beat heart rate (HR) patterns, e.g., Poincaré plots, provide information beyond traditional HRV, but such plots have not been used in mice. HR patterns from 3 min recording/ hour in 4 wild type and 4 PGC1α-deficient mice were compared. In comparison to normal mice, knockout mice tended to have lower HRs (694 ± 16 vs. 752 ± 51 bpm) consistent with their decreased ability to use glucose in the heart. Poincaré plots from each hour showed that none of the wild-type mice had abnormal, fan-like, complex patterns in any hour of their recording. However, 3 of the 4 knockout mice had a complex pattern in at least 10 hours of the recording. Results suggest that hourly Poincaré plot analyses from multiple short-term recordings may be useful in identifying cardiac autonomic abnormalities in knockout mouse models. Samples from the entire 24-hour period provide more information about autonomic function than a single brief recording.