An increasing number of patients worldwide suffer from bone fractures that occur after low intensity trauma. Such fractures are usually associated with advanced age and osteoporosis but changes on the bone tissue level happen also with immobilization, Paget’s disease of bone, and other metabolic disorders. Revealing the skeletal origins of increased bone fragility is a prerequisite to contribute to improved health monitoring, preventive and therapeutic strategies. In this context, analyzing bone quality indices including osteocyte characteristics in physiological and pathological conditions using functional imaging modalities and microanalyses may inform researchers and clinicians. The characteristics of osteocyte lacunae along the osseous matrix composition distinguishes healthy, aged and diseased bone. Osteocyte lacunar characteristics could be regarded as a vital marker for bone quality assessment and fracture risk.