Many sensors have been developed to measure physiological information in the toilet for healthcare management and disease prevention. These sensors require personal identification to classify toilet users, assuming that several people use the same toilet. We aimed to provide biometrics based on cardiovascular physiological information obtained from a toilet seat. An electrocardiogram was measured by the toilet seat, and personal identification was performed, as in the previous study. In this study, we developed a ballistocardiographic (BCG) monitoring system using two vibration sensors installed beneath a toilet seat. We recorded 70 BCGs from seven healthy males during their urination. Peaks H, I, J, K, and L of the BCGs were clearly obtained. Twenty-six features such as amplitude and interval were calculated from the BCG peaks. Personal identification was performed using the Mahalanobis distance, and the accuracy of identification and equal error rate (EER) were calculated. The average identification accuracy was found to be 92.2%, and the average EER was found to be 34.1%. Although the EER was not sufficiently low, the average accuracy suggested that the proposed method using a toilet seat could provide adequate biometrics for application in the healthcare system.