Heart rate variability (HRV) and/or baroreflex sensitivity (BRS) are reduced in many disease states, including hypertension, kidney disease and depression, and may signify an increased risk of cardiac mortality. It is not well described if reduced levels of HRV and/or BRS are comparable between different disease states. We compared HRV and BRS in conscious telemetered and urethane anaesthetised rodent models of hypertension (Spontaneously Hypertensive Rat [SHR, n=14]), kidney disease (Lewis Polycystic Kidney [LPK, (n=18]) and depression (Flinders Sensitive Line [FSL, n=11]), and their respective genetic controls (Wistar Kyoto [WKY; n=12], Lewis [n=14] and Sprague Dawley [SD; n=12]), to address the following questions: (1) Are HRV and BRS reduced in these rodent models of disease compared with their controls; (2) Do different disease models have similarly reduced HRV and BRS; (3) Is HRV and BRS similar amongst control strains; and (4) What effect does anaesthesia have. Our results indicate: (1) Only the LPK and FSL exhibited reductions in HRV or BRS compared with their controls. The LPK exhibited reduced HRV (all spectral components) and BRS under anaesthetised conditions, while the FSL exhibited reduced total and high frequency HRV power and BRS. BRS was reduced in conscious LPK and FSL; (2) HRV was similar between the SHR, LPK and FSL under anaesthetised and conscious conditions with the exception that high frequency power was lower in conscious FSL. BRS, however, differed among the diseased strains with BRS lowest in the LPK under anaesthesia and in the FSL under conscious conditions; (3) HRV and BRS parameters were generally similar among the control strains with the only notable difference being an increase in BRS in the WKY under conscious conditions and (4) Urethane anaesthesia had suppressive effects on HRV in all strains examined and reduced BRS in the LPK, WKY and Lewis. These results indicate that reductions in HRV can be observed in rodent models of disease under anaesthetised conditions, likely due to the suppressive actions of urethane on HRV that may be accentuated by disease. Reductions in BRS, however, could be observed irrespective of the anaesthetised/conscious state and may be a more reliable index to assess cardiac risk in rodent models of disease.