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Abstract Abnormal ovulation, marked by the incomplete release of eggs from the gonads, was observed in previous stripping seasons. This prompted an observational study to explore its causes and impact on egg production. During the 2021 stripping season (strain A 21), abnormal ovulation was evident, leading to reduced egg output (eggs released into the abdominal cavity, and therefore available for fertilization and production) and increased variability in egg quality. Fertilization rates dropped from a median of 97 % in the first week to only 25 % by week nine. In 2022, another stripping season was monitored, this time including two strains (A 22 and B 22). Strain A 22 exhibited similar trends to strain A 21, though the impact was less severe. This was due to strategic management decisions, including not extending the stripping season and adjusting the criteria for determining ovulation readiness. Strain B 22, however, displayed results more in line with expected Atlantic salmon production. This study does not aim to compare genetic strain performance but rather investigates differences in broodstock treatment. The key distinction was vaccination protocols: both strains received an oil-based intraperitoneal vaccine, but strain A also received an additional intraperitoneal water-based vaccine. Given that injection vaccines can cause inflammatory reactions, such as adhesions, and may contain endocrine disruptors, they are hypothesized to be the primary cause of the abnormal ovulation observed. While this study did not directly test vaccine effects, industry feedback strongly suggests a link between the abnormal ovulation observed and vaccination protocol, underscoring the need for greater awareness of vaccination protocols in broodstock management.