The early diagnosis of pulmonary cancer can significantly improve the survival rate of patients, where pulmonary nodules detection in computed tomography images plays an important role. In this article, we propose a novel pulmonary nodule detection system based on convolutional neural networks (CNN). Our system consists of two stages, pulmonary nodule candidate detection and false positive reduction. For candidate detection, we introduce Iterative Self-Organizing Data Analysis Techniques Algorithm (ISODATA) to Faster Region-based Convolutional Neural Network (Faster R-CNN) model. For false positive reduction, a three-dimensional convolutional neural network (3D-CNN) is employed to completely utilize the three-dimensional nature of CT images. In this network, Focal Loss is used to solve the class imbalance problem in this task. Experiments were conducted on LUNA16 dataset. The results show the preferable performance of the proposed system and the effectiveness of using ISODATA and Focal loss in pulmonary nodule detection is proved. © 2020 ACM.