Studying natural reading and its underlying attention processes requires devices that are able to provide precise measurements of gaze without rendering the reading activity unnatural. In this paper we propose an eye tracking system that can be used to conduct analyses of reading behavior in low constrained experimental settings. The system is designed for dual-camera-based head-mounted eye trackers and allows free head movements and note taking. The system is composed of three different modules. First, a 3D model-based gaze estimation method computes the reader’s gaze trajectory. Second, a document image retrieval algorithm is used to recognize document pages and extract annotations. Third, a systematic error correction procedure is used to post-calibrate the system parameters and compensate for spatial drifts. The validation results show that the proposed method is capable of extracting reliable gaze data when reading in low constrained experimental conditions.