The mRNA of the nuclear co-activator peroxisome proliferator-activated receptor-gamma co-activator-1 (PGC-1) increases during prolonged exercise and is influenced by carbohydrate availability. It is unknown if the increases in mRNA reflect the PGC-1protein nor if glycogen stores are an important regulator. Seven male subjects (23 ± 1.3 y, VO_2max 48.4 ± 0.8 mL kg^-1 min^-1) exercised to exhaustion (~2h) at 65% VO_2max followed by ingestion of either a high- (HC) or low-carbohydrate (LC) diet (7 or 2.9 g kg^-1 per day, respectively) for 52-h of recovery. Glycogen remained depressed in LC (P<0.05) while returning to resting levels by 24 h in HC. PGC-1 mRNA increased both at exhaustion (3-fold) and 2 h later (6.2-fold) (P<0.05), but returned to rest levels by 24 h. PGC-1 protein increased (P<0.05) 23% at exhaustion, and remained elevated for at least 24 h (P<0.05). While there was no direct treatment effect (HC vs. LC) for PGC-1 mRNA or protein, there was a linear relationship between the changes in glycogen and those in PGC-1 protein during exercise and recovery (r = -0.68, P<0.05). In contrast, PGC-1 did not increase with exercise, but rather decreased (P<0.05) below rest level at 24 and 52 h and the decrease was greater (P<0.05) in LC. PGC-1 protein content increased in prolonged exercise, and remained up-regulated for 24 h, but this could not have been predicted by the changes in mRNA. The isoform declined rather than increasing and this was greater when glycogen was not resynthesized to rest levels.