We sought to determine the molecular basis of elevations in aerobic metabolic capacity in the oxidative muscle and liver of Gasterosteus aculeatus in response to cold acclimation. Fishes were cold- or warm-acclimated for 9 wk and harvested on days 1, 2, and 3 and weeks 1, 4, and 9 of cold acclimation at 8 degrees C, and on day 1 and week 9 of warm acclimation at 20 degrees C. Mitochondrial volume density was quantified using transmission electron microscopy and stereological techniques in warm- and cold-acclimated fishes harvested after 9 wk at 20 or 8 degrees C. Changes in aerobic metabolic capacity were assessed by measuring the maximal activity of citrate synthase (CS) and cytochrome-c oxidase (COX) in fishes harvested throughout the acclimation period. Transcript levels of the aerobic metabolic genes CS, COXIII, and COXIV, and known regulators of mitochondrial biogenesis, including peroxisome proliferator-activated receptor-gamma coactivators-1alpha and -1beta (PGC-1alpha and PGC-1beta), nuclear respiratory factor-1 (NRF-1), and mitochondrial transcription factor-A were measured in fishes harvested throughout the acclimation period using quantitative real-time PCR. The maximal activities of CS and COX increased in response to cold acclimation in both tissues, but mitochondrial volume density only increased in oxidative muscle (P < 0.05). The time course for changes in aerobic metabolic capacity differed between liver and muscle. The expression of CS increased within 1 wk of cold acclimation in liver and was correlated with an increase in mRNA levels of NRF-1 and PGC-1beta. Transcript levels of aerobic metabolic genes increased later in oxidative muscle, between weeks 4 and 9 of cold acclimation and were correlated with an increase in mRNA levels of NRF-1 and PGC-1alpha. These results show that aerobic metabolic remodeling differs between liver and muscle in response to cold acclimation and may be triggered by different stimuli.