Background: To date, there are still 242 districts in Indonesia which remain endemic for malaria, mostly in the eastern region of the country. East Nusa Tenggara Province is one of the regions with the highest Annual Parasite Incidence (API) per 1,000 population, with none of the districts or cities being able to achieve malaria elimination even once. Hence, most of the pregnant women who live in the Asia-Pacific countries are at risk of Plasmodium vivax infection. There is also a notion that malaria infection could increase the risk of miscarriage. Therefore, we aimed to assess the risk factors of miscarriage in the malaria-endemic regions in Eastern Indonesia. Methods: A case-control study was conducted using data from the previous malaria study in East Nusa Tenggara. This study included 37 respondents with a history of miscarriage and 74 control subjects matched by age (±5 years) and sub-district. We assessed the correlation of socioeconomic status, malaria, anemia, body mass index, and glucose-6-phosphate dehydrogenase (G6PD) deficiency with miscarriage. Data were analyzed using bivariate and multivariate analysis with p-value <0.05 indicates that the variable has a significant effect. Results: A total of 111 women were included in this study with 37 respondents being the case group and 74 being the control group. The risk of developing miscarriage increased in lower socioeconomic status (OR 1.05; 95% CI: 0.45- 2.44), in malaria-positive (OR 1.40; 95% CI: 0.60-3.26), in the presence of anemia (OR 1.90; 95% CI: 0.82-4.45), and in abnormal BMI (OR 1.08; 95% CI: 0.47-2.46). Conclusion: Lower socioeconomic status, malaria-positive, anemia, and abnormal BMI showed a positive correlation with miscarriage in the malariaendemic area of East Nusa Tenggara, Indonesia.