The dowel bone graft fusion technique for the ankle is a well-known and useful method. However, clinical results of dowel bone graft for small joint fusion are unknown. The objective of the present study is to evaluate the effects of dowel bone graft technique for small joint arthrodesis in an in vivo arthrodesis of rabbit elbow model compared with the conventional arthrodesis technique (open, joint surface debridement, and internal fixation method). We assigned 28 young adult New Zealand white rabbits to one of two groups: Group 1, the conventional fusion technique group; Group 2, the dowel bone graft fusion technique group. We performed arthrodesis surgery in two different ways for each group. Eight weeks after the operation, specimens were harvested, radiographed, mechanically tested for torque to failure and stiffness, and evaluated for histology. Fusion rates were 77% (10/13) in Group 1 and 93% (13/14) in Group 2 (p = 0.326). Torque to failure showed a mean of 0.86 Nm in Group 1 and 0.77 Nm in Group 2 (p = 0.464). The mean value of stiffness was 0.11 Nm/deg in Group 1 and 0.11 Nm/deg in Group 2 (p = 0.832). In Group 2, histological examination showed residual cartilage absorption and inflammatory response in all cases. In this model, we have been unable to show a difference in either the union rate or strength of fusion between the two methods. However, the dowel bone graft technique is an easy and less invasive method and has some advantages over the conventional method.