Purpose: The purpose of this study was to compare the effectiveness of three methods of cell inoculation on cell growth and bone formation: inoculation of seed cells into the scaffolds from two sides (two-side inoculation method), inoculation of seed cells from one side (single-side inoculation method), and inoculation of a compound of seed cells and type 1 collagen gel from one side (type 1 collagen inoculation method). Materials and Methods: Bone marrow stromal cells were isolated from 1-month-old male New Zealand rabbits and implanted into three-dimensional chitosan/beta-tricalcium phosphate scaffolds using the three different methods. Cultures were analyzed by various methods. Results: The type 1 collagen group expressed the best uniformity of cell distribution among all the three methods during a 1-week culture period, and the two-side group expressed the best uniformity during a 2- to 3-week culture period. The number of inoculated cells in the type 1 collagen group outpaced that of the other groups. With respect to the depth of penetration of the inoculated cells, the cells of the type 1 collagen group were concentrated on the surface of the scaffold and formed multiple layers, whereas the two-side group accounted for the deepest cell penetration. Conclusion: The two-side inoculation method improves the number and distribution of seed cells in vitro and enhances the quality and rate of bone formation in vivo. This method is the most suitable seed method for bone tissue engineering. Keywords: bone marrow stromal cells, distribution, inoculation, scaffold