Open AccessThe goal of standard histomorphometry is to provide methods of qualitative description of tissue structure based on image data. Typical measurements include geometric areas, perimeters, length, angle of orientation, form factors, center of gravity coordinates etc. There are well-established procedures for deriving the aforementioned quantities from binary images. However, segmentation of in vivo images of trabecular bone poses a problem which has not been solved yet. Recent years have brought significant developments within an emerging field of “gray-level histomorphometry”. The general goal of gray-level histomorphometry is to provide procedures for measuring geometric areas, perimeters, length, angle of orientation, form factors, center of gravity coordinates etc. without the need for image segmentation. Although the field is not very mature yet, the collected results suggest that this approach opens new perspectives which should not be overlooked by the scientific community. In the present review we summarize the state-of-the-art within the 3D gray-level histomorphometry.