To avoid using sensors with low biocompatibility and low durability in implantable total artificial heart (TAH) systems, the authors previously proposed a new method for estimating instantaneous values of flow rate and pressure head on the basis of voltage, current, and rotational speed in a motor driven centrifugal pump. The previous in vitro experiments showed that the proposed estimator could automatically compensate for the effect of the change in blood viscosity on the estimation accuracy by employing two kinds of autoregressive exogenous models. In this study, validity and reliability of this estimation method were ascertained in an acute animal experiment. In the experiment, two centrifugal blood pumps were implanted into an adult goat as a total artificial heart. Results of estimation were compared with true values when blood viscosity was changed by injecting physiological saline. The results indicated that the system could successfully estimate pressure head by compensating the change of viscosity, although the estimation accuracy of the in vivo estimation was not so high as that of the previous in vitro tests.