In this paper, we present BinEye, an innovative tool which trains a system of three convolutional neural networks to characterize the authors of program binaries based on novel sets of features. The first set of features is obtained by converting an executable binary code into a gray image; the second by transforming each executable into a series of bytecode; and the third by representing each function in terms of its opcodes. By leveraging advances in deep learning, we are then able to characterize a large set of authors. This is accomplished even without the missing features and despite the complications arising from compilation. In fact, BinEye does not require any prior knowledge of the target binary. More important, an analysis of the model provides a satisfying explanation of the results obtained: BinEye is able to auto-learn each author’s coding style and thus characterize the authors of program binaries. We evaluated BinEye on large datasets extracted from selected open-source C++ projects in GitHub, Google Code Jam events, and several programming projects, comparing it wiexperimental results demonstrate that BinEye characterizes a larger number of authors with a significantly higher accuracy (above 90%). We also employed it in the context of several case studies. When applied to Zeus and Citadel, BinEye found that this pair might be associated with common authors. For other packages, BinEye demonstrated its ability to identify the presence of multiple authors in binary code.