BACKGROUND: The magnamosis, a minimal invasive, suture-free procedure, has been used for digestive tract or vessel reconstruction, such as gastrointestinal anastomosis, bilioenteric anastomosis, and coronary artery bypass. Although some case reports have demonstrated the potential of magnamosis for the treatment of congenital rectal atresia (RA), they cannot provide strong evidence for its widespread application. AIM: To assess the feasibility and safety of magnamosis in treating RA in dogs as compared to suturing anastomosis. The findings of this study can be beneficial in guiding the clinical application of magnamosis. METHODS: Thirty-six dogs were randomly assigned to the magnamosis group ( RESULTS: The mean time for rectal anastomosis was significantly shorter in the magnamosis group (12.22 ± 2.78 minutes) than the suturing anastomosis group (18.11 ± 1.68 minutes). There was one incidence of anastomotic bleeding in the suturing anastomosis group, whereas no complication was recorded in the magnamosis group. The magnets were discharged post-surgery in 7.17 ± 1.30 days in all the dogs. The histopathological examination revealed a smoother healing of anastomotic mucosa in the magnamosis group as compared to that in the suturing anastomosis group. Moreover, the fiber alignment was also more natural in the magnamosis group with minimal inflammation. CONCLUSION: Rectal reconstruction using magnamosis is a feasible, safe, and effective alternative to suturing anastomosis in dogs, with the added benefit of faster and more natural healing of the anastomosis.