Verbal autopsy (VA) is a widely used method for analyzing cause of death in absence of vital registration systems. We adapted the InterVA method to extrapolate causes of death for stillbirths and neonatal deaths from verbal autopsy questionnaires, using data from Malawi, Zimbabwe, and Nepal. We obtained 734 stillbirth and neonatal VAs from recent community studies in rural areas: 169 from Malawi, 385 from Nepal, and 180 from Zimbabwe. Initial refinement of the InterVA model was based on 100 physician-reviewed VAs from Malawi. InterVA indicators and matrix probabilities for cause of death were reviewed for clinical and epidemiological coherence by a pediatrician-researcher and an epidemiologist involved in the development of InterVA. The modified InterVA model was evaluated by comparing population-level cause-specific mortality fractions and individual agreement from two methods of interpretation (physician review and InterVA) for a further 69 VAs from Malawi, 385 from Nepal, and 180 from Zimbabwe. Case-by-case agreement between InterVA and reviewing physician diagnoses for 69 cases from Malawi, 180 cases from Zimbabwe, and 385 cases from Nepal were 83% (kappa 0.76 (0.75 - 0.80)), 71% (kappa 0.41(0.32-0.51)), and 74% (kappa 0.63 (0.60-0.63)), respectively. The proportion of stillbirths identified as fresh or macerated by the different methods of VA interpretation was similar in all three settings. Comparing across countries, the modified InterVA method found that proportions of preterm births and deaths due to infection were higher in Zimbabwe (44%) than in Malawi (28%) or Nepal (20%). The modified InterVA method provides plausible results for stillbirths and newborn deaths, broadly comparable to physician review but with the advantage of internal consistency. The method allows standardized cross-country comparisons and eliminates the inconsistencies of physician review in such comparisons.