Background: Women are more likely to be diagnosed with congenital anomalies. Following prenatal diagnosis of fetal abnormalities, women may be forced to make decisions about whether to continue a pregnancy with fetal abnormalities. This can be a dilemma for the women. The aim of the study was to explore women’s experiences of prenatal diagnosis of fetal abnormalities. Methods: A qualitative study was conducted in a referral women’s hospital in Tehran, Iran in 2018. Participants were a purposeful sample of 15 women with prenatal diagnosis of fetal abnormalities. Data were collected by individual, in-depth interviews. The conventional content analysis approach was used to analyze the data. Results: Two main themes “emotional suffering” and “decision-making challenge” were extracted from the participants’ experiences. Emotional suffering consisted of subthemes “sense of guilt”, “self-blame”, “questioning of God”, “commiseration” and “projection”. Decision making challenge included subthemes “distrust”, “possible cure”, “dark future”, “economic problems”, “stereotypical beliefs”, “coercion” and “lack of support”. Conclusions: The experience of prenatal diagnosis of fetal abnormalities was associated with emotional suffering and challenges in decision-making to continue or terminate the pregnancy. Strategies need to be employed to improve women’s autonomy in decision-making. Healthcare professionals should be trained in communication skills to provide appropriate counseling to support women with diagnosis of fetal anomalies.