The structure of cortical bone at the collagen-mineral level was investigated by means of atomic force microscopy. Surfaces of the specimens treated with collagenase and ethylenediaminetetraacetic acid (EDTA) were examined. Images of blob-like objects observed in intact specimen became clearly outlined after collagenase treatment; the sizes of the blob decreased, suggesting that each blob had been fragmented by the collagenase treatment. Following EDTA treatment of an intact specimen, an image of thread-like objects appeared; the thread was partly constructed by trains of blobs and the other parts of the threads had a periodic pattern along its longer axis. The period was almost equal to the collagen D-period of the Hodge–Petruska model, indicating that the threads are collagen fibrils and that the blobs are related to the mineral phase in bone. It was concluded that minerals were deposited on and along collagen fibrils. A decorated collagen fibril model for the spatial relationship between mineral and collagen fibril was proposed. According to our model, the mineral inside the collagen fibril is about one forth of the extrafibrillar mineral.