Background: It has not been established whether the clinical outcomes of tubal heterotopic pregnancy resulting from assisted conception are different to those of spontaneous conception. The aim of this study was to compare the clinical course and the outcome of intrauterine gestation following surgical treatment for tubal heterotopic pregnancy according to the method of pregnancy. Methods: Medical records of 13 cases of tubal heterotopic pregnancy experienced in Seoul National University Hospital during 1990–2004 and 30 case reports of tubal heterotopic pregnancy published in the Korean Journal of Obstetrics and Gynecology during 1980–2004 were reviewed retrospectively. The clinical outcomes were compared between the assisted (n = 23) and spontaneous conception groups (n = 20). Results: The assisted conception group had a significantly higher preoperative systolic blood pressure and a previous history of pelvic pathology. The spontaneous group had a higher incidence of tubal rupture and hemoperitoneum. The assisted conception group had a higher live birth rate than the spontaneous group (47.8 vs. 20%, p = 0.056). Conclusions: In tubal heterotopic pregnancy, the assisted conception group had a more favorable clinical course and intrauterine gestation outcome following surgical treatment when compared with the spontaneous conception group.