A longitudinal study investigated the courses of mortality in commercial free-range organic layer flocks in Denmark. In total, 15 organic egg-producing flocks from 11 farms were randomly selected among 80 farms registered in Denmark. Four farms with confined egg production on deep litter were included for comparison. Flock sizes ranged from 2260 to 5940 layers. The flocks were monitored from introduction to the layer farm until slaughter. Flock mortalities ranged from approximately 2% to 91%, with a mean of 20.8% for organic flocks compared with 7% for confined flocks on deep litter. In total, 4608 layers were submitted for postmortem examination, representing >40% of all the dead layers in the investigated flocks. Outbreaks of erysipelas (Erysipelothrix rhusiopathiae) and fowl cholera (Pasteurella multocida) were observed in two and three organic flocks, respectively. The mortality rate reached 91% in one organic flock dually affected by erysipelas and fowl cholera. In six organic flocks, outbreaks of blackhead were diagnosed. Concurrent infections of erysipelas and blackhead were diagnosed in one organic flock. Escherichia coli infections in the form of septicemia were identified in all organic flocks. In addition, cannibalism and constipation contributed significantly to the mortality in some organic flocks. In the confined deep litter flocks, E. coli infection, constipation, and cannibalism represented the most common causes of mortality.