This dissertation focuses on the three-dimensional high-resolution micro-structure of bone. Although bone tissue – a complex hierarchical material – has been investigated for more than 300 years, many structural and physiological aspects of bone remain obscure. The aim of this work is to determine the collagen fibril organization in lamellar bone using threedimensional imaging and quantitative analysis and to test the possibility that nascent functional adaptations of bone can be detected at the level of lamellar structure. The major finding of this work is the identification of a previously unknown structural component embedded in bone tissue – a built-in disordered motif (material) that occupies about 15-20% of the volume. The disordered material is closely associated with the cellular component of bone tissue and hence presumably plays an important role in bone homeostasis. Comparison of the collagen microarchitecture of lamellae in circumferential and osteonal compact bone and in trabecular bone of humans did not reveal substantial differences at the micron-scale. However, the tissue structural characteristics of trabecular bone (millimeter scale) were found to be reflected at the level of collagen fibril array (micron scale) 3D organization. The methodology developed can be widely used in skeletal biology and other fields of research.