The aim of the present study was to design a computer program (based on the ConnEulor principle) for direct measurement of 3-D connectivity density in iliac crest bone sections, as used for conventional histomorphometry. We used the physical disector principle and developed an algorithm for nonlinear alignment of the disector pairs. 3-D connectivity was evaluated in transiliac specimens from 30 nonselected autopsy cases of 14 men (age range 20-84 years) and 16 women (age range 20-96 years). In order to visualize the findings from the disector pairs, 3-D reconstruction was performed for two of the iliac crest biopsies. The designed computer program aligns the two sections forming a disector pair and automatically depicts the differences between the images, thereby making correct, direct connectivity density measurements available for conventional bone research.