Determination of sex of human skeletons is a fundamental issue in physical anthropology. The purpose of this study is to develop new standards to determine the sex of fragmentary human skeletal remains from archaeological sites in Japan. In order to accomplish this, we measured the head and neck circumferences of long bones of medieval Japanese skeletons, and provided metric diagnosis of sex using discriminant function analysis. The materials are comprised of human skeletal remains from the Yuigahama-minami site, Kamakura, Japan. The sample size used in this study is 54 males and 51 females, which were excavated from individual burial graves. The accuracy of sex classification is 85.1-93.6% for discriminant functions with only one variable, and reaches 93.9% for those with a combination of two variables. It is noteworthy that new standards allowing for reliable diagnosis are developed with a small number of variables from well preserved parts of the ancient skeletons themselves. The results here will provide reliable diagnostic standards of fragmentary skeletons.