KNI-472 is the first anesthetic system for mice and rats to incorporate a ventilator. It consists of a newly developed syringe pump-type vaporizer and gas monitor that can deliver accurate concentrations of anesthetic gas at an extremely low airflow. In this study, we compared the hemodynamic effects of isoflurane anesthesia using KNI-472 and intraperitoneal pentobarbital anesthesia. In the isoflurane anesthetic group, Institute of Cancer Research (ICR) mice were anesthetized with 5% isoflurane, followed by endotracheal intubation. Subsequently, they were ventilated mechanically, and anesthesia was maintained with 2% isoflurane for a 60-min period using KNI-472. In the pentobarbital anesthetic group, the ICR mice were anesthetized by an intraperitoneal injection of sodium pentobarbital (70 mg/kg). In isoflurane anesthesia, the heart rate (HR) and mean blood pressure (MBP) were stable. In contrast, in pentobarbital anesthesia, MBP decreased in the first stage after the initiation of anesthesia, after which it gradually increased. The intra-group variability in the estimated skin blood flow (SBF) was higher in the pentobarbital anesthesia than that in the isoflurane anesthesia. The PaO(2) and PaCO(2) values at 15 min after the initiation of pentobarbital anesthesia revealed hypoxia and hypercapnia compared with isoflurane anesthesia. In this study, isoflurane anesthesia using KNI-472, unlike pentobarbital anesthesia, did not induce changes in MBP, SBF, or blood gases. The changes induced by pentobarbital anesthesia were attributed to a change in the depth of anesthesia with time. These results indicate that inhalation anesthesia using KNI-472 is suitable in research on the hemodynamic state in mice.