The aim of this study was to investigate whether the bone response to long bed rest–related immobility and during subsequent recovery differed at anatomically different sectors of tibial epiphysis and diaphysis. For this study, peripheral quantitative tomographic (pQCT) scans obtained from a previous 90-day ‘Long Term Bed Rest’ intervention were preprocessed with a new method based on statistical approach and re-analysed sector-wise. The pQCT was performed on 25 young healthy males twice before the bed rest, after the bed rest and after 1-year follow-up. All men underwent a strict bed rest intervention, and in addition, seven of them received pamidronate treatment and nine did flywheel exercises as countermeasures against disuse-related bone loss. Clearly, 3–9% sector-specific losses in trabecular density were observed at the tibial epiphysis on average. Similarly, cortical density decreased in a sector-specific way being the largest at the anterior sector of tibial diaphysis. During recovery, the bed rest–induced bone losses were practically restored and no consistent sector-specific modulation was observed in any subgroup. It is concluded that the sector-specific analysis of bone cross-sections has potential to reveal skeletal responses to various interventions that cannot be inferred from the average analysis of the whole bone cross-section. This approach is considered also useful for evaluating the bone responses from the biomechanical point of view.