Breath-by-breath measurements of end-tidal O(2) and CO(2) concentrations in harbor porpoise reveal that the respiratory gas exchange ratio (R(R); CO(2) output/O(2) uptake) of the first lung ventilation in a breathing bout after a prolonged breath-hold is always well below the animal's metabolic respiratory quotient (RQ) of 0.85. Thus the longest apneic pauses are always followed by an initial breath having a very low R(R) (0.6-0.7), which thereafter increases with each subsequent breath to values in excess of 1.2. Although the O(2) stores of the body are fully readjusted after the first three to four breaths following a prolonged apneic pause, a further three to four ventilations are always needed, not to load more O(2) but to eliminate built-up levels of CO(2). The slower readjustment of CO(2) stores relates to their greater magnitude and to the fact that they must be mobilized from comparatively large and chemically complex HCO/CO(2) stores that are built up in the blood and tissues during the breath-hold. These data, and similar measurements on gray seals (12), indicate that it is the readjustment of metabolic RQ and not O(2) stores per se that governs the amount of time an animal must spend ventilating at the surface after a dive.