Interventions such as chronic electrical stimulation may not realistically replicate the effects of exercise on skeletal muscle. So, we used an animal model of intensity-controlled running, similar to that undertaken by humans, to investigate mechanistic changes induced by exercise. Wistar rats (312 ± 13 g) were familiarised with running on a motorised treadmill within a metabolic chamber. Ambient air was pumped through the chamber and analysed for concentrations of oxygen and carbon dioxide (Oxymax system; Columbus Instruments, OH, USA), which were used to calculate the animal’s oxygen uptake. Each animal’s maximum oxygen uptake ([vdot]O₂max) was measured, using an incremental exercise test, before and after the exercise intervention. Rats in the exercise group ran for 30 min at a speed and incline equivalent to 70-75% of their [vdot]O₂max (preceded and followed by 5 min warm-up and cool-down), 4 days per week for 5 weeks. On the same days, control animals undertook the warm-up and cool-down exercise (10 min at a treadmill speed equivalent to 35-40% [vdot]O₂max). Animals were killed 48 h after the final exercise test and their plantaris muscles harvested. Fibre type proportions were determined from myosin-ATPase stained cryosections and changes in the muscle proteome were investigated using 1-D electrophoresis and mass spectrometry (1). Data are presented as means ± SD (n = 5, per group) and significant differences were determined using Student’s two-tailed independent t test. Before the intervention the average [vdot]O₂max was 40.8 ± 2.2 ml kg^-1 min^-1 with no significant difference between control and exercise animals. After the exercise intervention the [vdot]O₂max of the trained animals (46.7 ± 0.5 ml kg^-1 min^-1) had increased 11% (P = 0.008) over that of control animals (42.2 ± 2.8 ml kg^-1 min^-1). Exercise did not alter muscle protein content, but there was a suggestion of a greater (25%; P = 0.22) area fraction of slow-oxidative fibres. Densitometry of gel images identified 37 protein bands; one of which (~60 kDa) was significantly reduced (37%; P = 0.056) in plantaris of exercised rats. Database searches (MASCOT; Matrix Science) of the peptide mass fingerprint identified this band as phosphoglucomutase 1, based on 25 matched queries with a MOWSE score of 177 (MOWSE score >63 being significant P<0.05). This enzyme catalyses the reversible reaction glucose 1-phosphate to glucose 6-phosphate, a decrease in the abundance of which signifies a lesser reliance on glycogen metabolism to fuel this intensity of exercise. In conclusion, intensity-controlled running increased the animals [vdot]O₂max and altered their skeletal muscle metabolism.