BackgroundSexual dimorphism is obvious not only in the overall architecture of human body, but also in intraoral details. Many studies have found a correlation between gender and morphometric features of teeth, such as mesio-distal diameter, buccal-lingual diameter and height. However, it’s still difficult to detect gender through the observation of intraoral photographs, with accuracy around 50%. The purpose of this study was to explore the possibility of automatically telling gender from intraoral photographs by deep neural network, and to provide a novel angle for individual oral treatment.MethodsA deep learning model based on R-net was proposed, using the largest dataset (10,000 intraoral images) to support the automatic detection of gender. In order to reverse analyze the classification basis of neural network, Gradient-weighted Class Activation Mapping (Grad-CAM) was used in the second step, exploring anatomical factors associated with gender recognizability. The simulated modification of images based on features suggested was then conducted to verify the importance of characteristics between two genders. Precision (specificity), recall (sensitivity) and receiver operating characteristic (ROC) curves were used to evaluate the performance of our network. Chi-square test was used to evaluate intergroup difference. A value of p < 0.05 was considered statistically significant.ResultsThe deep learning model showed a strong ability to learn features from intraoral images compared with human experts, with an accuracy of 86.5% and 82.5% in uncropped image data group and cropped image data group respectively. Compared with hard tissue exposed in the mouth, gender difference in areas covered by soft tissue was easier to identify, and more significant in mandibular region than in maxillary region. For photographs with simulated removal of lips and basal bone along with overlapping gingiva, mandibular anterior teeth had similar importance for sex determination as maxillary anterior teeth.ConclusionsDeep learning method could detect gender from intraoral photographs with high efficiency and accuracy. With assistance of Grad-CAM, the classification basis of neural network was deciphered, which provided a more precise entry point for individualization of prosthodontic, periodontal and orthodontic treatments.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12903-023-03033-8.