The inclusion of biological and ecological aspects in the assessment of fish population status is one of the bases for an ecosystem-based fisheries management. During the past two decades the Eastern Baltic cod has experienced a drastic reduction in growth and body condition that may have affected its survival. We used results from published experimental literature linking cod condition to starvation and mortality, to estimate the annual proportion of cod close to the lethal condition level in the Eastern Baltic cod stock. Thereafter we applied these results to adjust the natural mortality (M) assumed in the analytical stock assessment model. The results in terms of Spawning Stock Biomass (SSB), Fishing mortality (F) and Recruitment (R) in the final year from the stock assessment using M values adjusted for low condition were up to 40% different compared with the assessment assuming a constant M = 0.2. This method could be used for adjusting natural mortalities for other cod stocks where changes in condition are observed.