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Understanding reproductive physiology in mysticetes has been slowed by the lack of repeated samples from individuals. Analysis of humpback whale baleen enables retrospective hormone analysis within individuals dating back 3–5 years before death. Using this method, we investigated differences in four steroid hormones involved in reproduction and mating during confirmed pregnant and non-pregnant periods in two female humpback whales (Megaptera novaeangliae) with known reproductive histories based on sightings and necropsy data. Cortisol, corticosterone, testosterone, and estradiol concentrations were determined via enzyme immunoassay using subsamples of each baleen plate at 2 cm intervals. There were no significant differences in cortisol or corticosterone during pregnancy when compared to non-pregnancy (inter-calving interval), but there were significant differences between the two whales in average glucocorticoid concentrations, with the younger whale showing higher values overall. For testosterone, levels for the younger female peaked at parturition in one pregnancy, but also had spikes during non-pregnancy. The older female had three large spikes in testosterone, one of which was associated with parturition. Estradiol had large fluctuations in both whales but had generally lower concentrations during non-pregnancy than during pregnancy. There were peaks in estradiol before each pregnancy, possibly coinciding with ovulation, and peaks coinciding with the month of parturition. Both estradiol and testosterone could be useful for determining ovulation or impending birth. Using baleen to investigate retrospective steroid hormone profiles can be used for elucidating long-term patterns of physiological change during gestation. Lay summary Case studies of two pregnant humpback whales whose hormones were analyzed in baleen may illuminate when humpback whales ovulate, gestate, and give birth. These physiological metrics could assist in accurate population growth assessments and conservation of the species. This study shows that baleen hormone analysis can be a useful tool for understanding whale reproductive physiology. [ABSTRACT FROM AUTHOR]