Objective: To measure heart rate variability metrics in critically ill COVID-19 patients with comparison to all-cause critically ill sepsis patients. Design and patients: Retrospective analysis of COVID-19 patients admitted to an ICU for at least 24h at any of Emory Healthcare ICUs between March and April 2020. The comparison group was a cohort of all-cause sepsis patients prior to COVID-19 pandemic. Interventions: none. Measurements: Continuous waveforms were captured from the patient monitor. The EKG was then analyzed for each patient over a 300 second (s) observational window, that was shifted by 30s in each iteration from admission till discharge. A total of 23 HRV metrics were extracted in each iteration. We use the Kruskal-Wallis and Steel-Dwass tests (p < 0.05) for statistical analysis and interpretations of HRV multiple measures. Results: A total of 141 critically-ill COVID-19 patients met inclusion criteria, who were compared to 208 patients with all-cause sepsis. Demographic parameters were similar apart from a high proportion of African-Americans in the COVID-19 cohort. Three non-linear markers, including SD1:SD2, sample entropy, approximate entropy and four linear features mode of Beat-to-Beat interval (NN), Acceleration Capacity (AC), Deceleration Capacity (DC), and pNN50, were statistical significance between more than one binary combinations of the sub-groups (comparing survivors and non-survivors in both the COVID-19 and sepsis cohorts). The three nonlinear features and AC, DC, and NN (mode) were statistically significant across all four combinations. Temporal analysis of the main markers showed low variability across the 5 days of analysis, compared with sepsis patients. Conclusions: Heart rate variability is broadly implicated across patients infected with SARS-CoV-2, and admitted to the ICU for critical illness. Comparing these metrics to patients with all-cause sepsis suggests a unique set of expressions that differentiate this viral phenotype. This finding could be investigated further as a potential biomarker to predict poor outcome in this patient population, and could also be a starting point to measure potential autonomic dysfunction in COVID-19.