High and variable mortality during the egg and larval stages is thought to be an important source of interannual variability in stock size in many marine fish. However, quantitative information about the mortality during these life stages, especially interannual variability, is sparse. Here, we used a time-series covering 35 years (1959-1993) of survey data to estimate mortality during the egg stages of northeast Arctic cod (Gadus morhua) and Northeast Arctic haddock (Melanogrammus aeglefinus). Using a regression approach based on the numbers of eggs in different developmental stages, we calculated the mean instantaneous mortality rate of cod eggs to be 0.17 d−1 (95% CI: 0.15-0.19), which is significantly higher than that for haddock, 0.09 d−1 (95% CI: 0.07-0.12). Interannual variability in egg mortality ranges from ∼0.12 to ∼0.22 d−1 for cod and from ∼0.04 to ∼0.12 d−1 for haddock. The accuracy of these estimates was evaluated by the analysis of synthetic data constructed from a coupled physical-biological model, suggesting that mean mortality and the magnitude of interannual variability were estimated reliably, but not mortality for any given year.