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Southern hemisphere humpback whales undertake the longest migrations and associated periods of fasting of any mammal. Fluctuations in lipid energy stores are known to profoundly affect the toxicokinetics of lipophilic organochlorine compound (OC) burdens. Results from blubber biopsy sampling of adult, male humpback whales at two time points of the annual migration journey revealed dramatic concentration effects for the majority of OC compounds. The observed concentration effect was, however, not linear with measured average blubber lipid loss indicating significant redistribution of OCs and hence the importance of alternate lipid depots for meeting the energetic demands of the migration journey. Applying lipophilic OC burdens as novel tracers of whole-body lipid dynamics, the observed average concentration index suggests an average individual weight loss of 13% over 4 months of the migration journey. This value is based upon lipid derived energy and is in good agreement with previous weight prediction formulas. Notably, however, these estimates may greatly underestimate individual weight loss if significant protein catabolism occurs. Biomagnification factors between migrating southern hemisphere humpback whales and their principal prey item, Antarctic krill, closely resembled those of baleen whales feeding on herbivorous zooplankton in the Arctic. This study emphasizes the importance of considering prolonged periods of food deprivation when assessing chemical risks posed to wildlife. This is of particular importance for Polar biota adapted to extremes in ecosystem productivity.