The present study examined the three-dimensional process of collagen fibril formation in the human osteosarcoma cell line NOS-1 by conventional scanning electron microscopy (SEM) and atomic force microscopy (AFM). SEM images showed collagen fibril formation on the bottom of culture dishes after 1 week of culture. The collagen fibrils had diameters of 30-100 nm. The surfaces of individual fibrils had characteristic grooves and ridges with periodicities of 60-70 nm. AFM images showed that the newly formed collagen fibrils were 30-300 nm in diameter and possessed characteristic grooves and ridges with periodicities of 60-70 nm. The thicker collagen fibrils contained thinner (approximately 30 nm thick) subfibrils that ran in a helical direction along the long axis of the thicker fibrils. Furthermore, twisted structures of collagen fibrils, which possessed a characteristic rope-like structure, were also identified. The ultrastructure of the collagen fibrils was clearly imaged in liquid medium by AFM, and the process of collagen fibril assembly was successfully analyzed under conditions much closer to the physiological state than those afforded by transmission electron microscopy or SEM. AFM also provided a precise morphological measurement, particularly of the vertical distance, of collagen fibrils with nanometer-scale resolution in liquid conditions.