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Abstract Introduction A heterotopic pregnancy is defined as the presence of a combined intrauterine and ectopic pregnancy. Its estimated incidence is accepted as between 1/7000 and 1/30,000 pregnancies. It is also reported to be as high as 1% after the use of assisted reproductive technology, but Clomiphene Citrate which increases the rate of twinning, could be associated with a heterotopic pregnancy rate of 1/900, which is much less than using assisted reproductive technology. Heterotopic pregnancies are diagnostic and therapeutic challenges for obstetricians. If they continue without diagnosis, a life-threatening situation may occur even when surgical intervention with laparotomy is performed. Case presentation We present the case of a 22-year-old Iranian woman who developed a simultaneous extra -and intrauterine pregnancy after the induction of ovulation with Clomiphene. In this case, there was a delay in the detection of the ectopic pregnancy component resulting in an emergency laparotomy being performed. Fortunately after the laparotomy, the intrauterine pregnancy was not affected and it progressed satisfactorily until 37 weeks. A healthy male baby was delivered by caesarean section. Conclusion This case suggests that a heterotopic pregnancy must always be considered in patients presenting with pelvic pain even in a confirmed intrauterine pregnancy, particularly after the induction of ovulation by Clomiphene Citrate or assisted reproductive technology. Every clinician treating women of reproductive age should keep this diagnosis in mind. It also demonstrates that early diagnosis is essential in order to salvage the intrauterine pregnancy and avoid maternal morbidity and mortality.