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Background: Each year, 1.2 million intrapartum stillbirths occur globally. In Nepal, about 50 % of the total number of stillbirths occur during the intrapartum period. An understanding of the risk factors associated with intrapartum stillbirth will facilitate the development of preventative strategies to reduce the associated burden of death. This study was conducted in a tertiary-care setting with the aim to identify risk factors associated with intrapartum stillbirth. Methods: A case-control study was completed from July 2012 to September 2013. All women who had an intrapartum stillbirth during the study period were included as cases, and 20 % of women with live births were randomly selected upon admission to create the referent population. Relevant information was retrieved from clinical records for case and referent women. In addition, interviews were completed with each woman to determine their demographic and obstetric history. Results: During the study period, 4,476 women were enrolled as referents and 136 women had intrapartum stillbirths. The following factors were found to be associated with an increased risk for intrapartum stillbirth: poor familial wealth quintile (Adj OR 1.8, 95 % CI-1.1-3.4); less maternal education (Adj OR, 3.2 95 % CI-1.8-5.5); lack of antenatal care (Adj OR, 4.8 95 % CI 3.2-7.2); antepartum hemorrhage (Adj OR 2.1, 95 % CI 1.1-4.2); multiple births (Adj. OR-3.0, 95 % CI- 1.9-5.4); obstetric complication during labor (Adj. OR 4.5, 95 % CI-2.9-6.9); lack of fetal heart rate monitoring per protocol (Adj. OR-1.9, 95 % CI 1.5-2.4); lack of partogram use (Adj. OR-2.1, 95 % CI 1.1-4.1); small-for-gestational age (Adj. OR-1.8, 95 % CI-1.2-1.7); preterm birth (Adj. OR-5.4, 95 % CI 3.5-8.2); and being born preterm with a small-for-gestational age (Adj. OR-9.0, 95 % CI 7.3-15.5). Conclusion: Being born preterm with a small-for-gestational age was associated with the highest risk for intrapartum stillbirth. Inadequate fetal heart rate monitoring and partogram use are preventable risk factors associated with intrapartum stillbirth; by increasing adherence to these interventions the risk of intrapartum stillbirth can be reduced. The association of the lack of appropriate antenatal care with intrapartum stillbirth indicates that quality antenatal care may improve fetal health and outcomes. Trial registration: ISRCTN97846009 [ABSTRACT FROM AUTHOR]