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A few epidemiologic studies have reported an association between nitrate in drinking water and the risk of birth defects (BD). Our objective was to examine this association in a large, population-based study with individual-level exposure estimates. We studied a cohort of all Danish singletons liveborn to Danish-born parents from 1991–2013 (N=1,018,914). In total, 33,182 BD diagnosed until the age of two were identified. Nitrate concentrations during pregnancy were analyzed using continuous and categorical variables. Odd ratios (OR) and 95% confidence intervals (95% CI) were estimated using logistic regression with generalized estimating equations and controlling for parental age, birth year, birth order, maternal smoking, education, employment, and income. Analyses were conducted for ten major BD categories, and for subcategories that were of interest.