Sex determination from skeletons is an important research subject in forensic medicine. Previous skeletal sex assessments are through subjective visual analysis by anthropologists or metric analysis of sexually dimorphic features. In this work, we present an automatic sex determination method for 3D digital skulls, in which a statistical shape model for skulls is constructed, which projects the high-dimensional skull data into a low-dimensional shape space, and Fisher discriminant analysis is used to classify skulls in the shape space. This method combines the advantages of metrical and morphological methods. It is easy to use without professional qualification and tedious manual measurement. With a group of Chinese skulls including 127 males and 81 females, we choose 92 males and 58 females to establish the discriminant model and validate the model with the other skulls. The correct rate is 95.7% and 91.4% for females and males, respectively. Leave-one-out test also shows that the method has a high accuracy.