Purpose: Minimally invasive interventions offer benefits for patients, while also entailing drawbacks for surgeons, such as the loss of depth perception. Thus estimating distances, which is of particular importance in gastric bypasses, becomes difficult. In this paper, we propose an approach based on stereo endoscopy that segments organs on-the-fly and measures along their surface during a minimally invasive interventions. Here, the application of determining the length of bowel segments during a laparoscopic bariatric gastric bypass is the main focus, but the proposed method can easily be used for other types of measurements, e.g., the size of a hernia. Methods: As input, image pairs from a calibrated stereo endoscope are used. Our proposed method is then divided into three steps: First, we located structures of interest, such as organs and instruments, via random forest segmentation. Two modes of instrument detection are used. The first mode is based on an automatic segmentation, and the second mode uses input from the user. These regions are then reconstructed, and the distance along the surface of the reconstruction is measured. For measurement, we propose three methods. The first one is based on the direct distance of the instruments, while the second one finds the shortest path along a surface. The third method smooths the shortest path with a spline interpolation. Our measuring system is currently one shot, meaning a signal to begin a measurement is required. Results: To evaluate our approach, data sets from multiple users were recorded during minimally invasive bowel measurements performed on phantoms and pigs. On the phantom data sets, the overall average error was (Formula presented.) on shorter pieces of bowel ((Formula presented.)5 cm) and (Formula presented.) on longer pieces ((Formula presented.)10 cm). On the porcine data sets, the average error was (Formula presented.). Conclusion: We present and evaluate a novel approach that makes measuring on-the-fly during minimally invasive surgery possible. Furthermore, we compare different methods for determining the length of bowel segments. The only requirement for our approach is a calibrated stereo endoscope, thereby keeping the impact on the surgical workflow to a minimum.