Existing population models for humpback whales assume that all individuals within a population undertake the annual migration from feeding areas in high latitudes to breeding areas in tropical waters. An excess of males was recorded in the commercial whaling catches near breeding areas in the southern hemisphere, but no account of this was taken in developing population models, because it was believed that this bias was a result of whalers selecting against females with young calves. Here we demonstrate that the sex ratio of migrating humpback whales near a breeding area is highly skewed towards males. A biopsy study carried out in 1992 throughout the northward and southward migrations revealed a sex ratio of 2.4 males: 1 female in the population of humpback whales migrating along the east Australian coast (n = 180). A reanalysis of the catches made during commercial whaling in this and other areas of the southern hemisphere gave a sex ratio of the same order. The most plausible explanation, supported by some evidence, is that some females remain in the feeding areas throughout winter. The results reported here show that existing management models require major revision to take account of these findings.