High altitude pregnancy is associated with increased frequency of low birthweight infants and neonatal complications, the risks of which are higher in women of low-altitude ancestry. Does ancestry also influence the risk of miscarriage (pregnancy loss <20 weeks) in high-altitude pregnancy? To answer this, 5386 women from La Paz, Bolivia (3300-4150m) with ≥1 live-born infant were identified. Data were extracted from medical records including maternal and paternal ancestry, demographic factors, and reproductive history. Risk of miscarriage by ancestry was assessed using multivariate logistic regression, adjusting for parity and maternal age. Andean women experienced first live-births younger than Mestizo or European women (21.7±4.6 vs. 23.4±8.0 vs. 24.1±5.1, p<0.001). Andeans experienced more pregnancies per year of reproductive life (p<0.001) and had significantly higher ratios of live-births to miscarriages than women of Mestizo or European ancestry (p<0.001). Andean women were 24% less likely to have ever experienced a miscarriage compared to European women (OR:0.76; CI:0.62-0.90, p<0.001). The woman’s partner’s ancestry wasn’t a significant independent predictor of miscarriage. In conclusion, the risk of miscarriage at high altitude is lower in Andean women. The lack of a paternal ancestry effect suggests underlying mechanisms relate more to differential maternal adaptation in early pregnancy than fetal genetics.