In pelvic organ prolapse (POP), the organs are pushed downward along the lines of gravity, so measurements along this longitudinal body axis are desirable. We propose a universally applicable 3D coordinate system that corrects for changes in pelvic inclination and that allows the localization of any point in the pelvis at rest or under dynamic conditions on magnetic resonance images (MRI) of pelvic floor disorders in a scanner- and software independent manner. The proposed 3D coordinate system called 3D Pelvic Inclination Correction System (PICS) is constructed utilizing four bony landmark points, with the origin set at the inferior pubic point, and three additional points at the sacrum (sacrococcygeal joint) and both ischial spines, which are clearly visible on MRI images. The feasibility and applicability of the moving frame was evaluated using MRI datasets from five women with pelvic organ prolapse, three undergoing static MRI and two undergoing dynamic MRI of the pelvic floor in a supine position. The construction of the coordinate system was performed utilizing the selected landmarks, with an initial implementation completed in MATLAB. In all cases the selected landmarks were clearly visible, with the construction of the 3D PICS and measurement of pelvic organ positions performed without difficulty. The resulting distance from the organ position to the horizontal PICS plane was compared to a traditional measure based on standard measurements in 2D slices. The two approaches demonstrated good agreement in each of the cases. The developed approach makes quantitative assessment of pelvic organ position in a physiologically relevant 3D coordinate system possible independent of pelvic movement relative to the scanner. It allows the accurate study of the physiologic range of organ location along the body axis ("up or down") as well as defects of the pelvic sidewall or birth-related pelvic floor injuries outside the midsagittal plane, not possible before in a 2D reference line system. Measures in 3D can be monitored over time and may reveal pathology before bothersome symptoms appear, as well as allowing comparison of outcomes between different patient pools after different surgical approaches.