Background: The early diagnosis and treatment of heterotopic pregnancy (HP) remain one of the biggest challenges in the field of gynecology. A coexisting intrauterine gestation makes the ectopic pregnancy in HP more difficult to diagnose. This case series analysis is designed to explore factors affecting the incidence of HP secondary to in vitro fertilization-embryo transfer (IVF-ET) and that affecting pregnancy outcomes after surgical treatment of HP.Methods: From the IVF registry system, the clinical data of 29 patients with HP and 92 with an intrauterine-only pregnancy (IUP) following embryo transfer from January 2009 to December 2017 were retrospectively analyzed.Results HP had a higher proportion of previous ectopic pregnancies, multiple abortion history ( ≧ 2 times) and tubal indication for IVF than IUP. In patients with HP, 31.03% had spontaneous abortion, 25.00% had preterm delivery and 58.62% resulted in a live birth. According to the results from logistic regression, history of multiple abortions (odds ratio (OR) 3.031, 95% confidence intervals (CI) 1.087-8.453; P=0.034), tubal infertility (OR 3.844, 95% CI 1.268-11.656; P=0.017), previous ectopic pregnancies (OR 2.303, 95% CI 0.625-8.490; P=0.021) and multiple embryo transfer ( OR 0.300, 95% CI 0.092-0.983; P=0.037) resulted in an elevated proportion of HP in IVF cycles. Incidence of HP was comparable between patients transferred with blastocyst and cleavage embryos. Shorter operative duration, smaller size of the ectopic mass and location in the ampulla of the fallopian tube were associated with higher chance of survival in the coexistent intrauterine pregnancy after surgical treatment with HP.Conclusions:The early diagnosis of HP remains a challenge. Previous history of ectopic pregnancy, multiple abortions, tubal infertility and multiple embryo transfer may be considered as meaningful risk factors of subsequent HP following IVF-ET. In patients with HP treated by surgery, shorter operative duration, smaller size of the ectopic mass and location in the ampulla of the fallopian tube means better reproductive prognosis.