We determined the effects of a cycle training program in which selected sessions were performed with low muscle glycogen content on training capacity and subsequent endurance performance, whole body substrate oxidation during submaximal exercise, and several mitochondrial enzymes and signaling proteins with putative roles in promoting training adaptation. Seven endurance-trained cyclists/triathletes trained daily (High) alternating between 100-min steady-state aerobic rides (AT) one day, followed by a high-intensity interval training session (HIT; 8 x 5 min at maximum self-selected effort) the next day. Another seven subjects trained twice every second day (Low), first undertaking AT, then 1-2 h later, the HIT. These training schedules were maintained for 3 wk. Forty-eight hours before and after the first and last training sessions, all subjects completed a 60-min steady-state ride (60SS) followed by a 60-min performance trial. Muscle biopsies were taken before and after 60SS, and rates of substrate oxidation were determined throughout this ride. Resting muscle glycogen concentration (412 +/- 51 vs. 577 +/- 34 micromol/g dry wt), rates of whole body fat oxidation during 60SS (1,261 +/- 247 vs. 1,698 +/- 174 micromol.kg(-1).60 min(-1)), the maximal activities of citrate synthase (45 +/- 2 vs. 54 +/- 1 mmol.kg dry wt(-1).min(-1)), and beta-hydroxyacyl-CoA-dehydrogenase (18 +/- 2 vs. 23 +/- 2 mmol.kg dry wt(-1).min(-1)) along with the total protein content of cytochrome c oxidase subunit IV were increased only in Low (all P < 0.05). Mitochondrial DNA content and peroxisome proliferator-activated receptor-gamma coactivator-1alpha protein levels were unchanged in both groups after training. Cycling performance improved by approximately 10% in both Low and High. We conclude that compared with training daily, training twice every second day compromised high-intensity training capacity. While selected markers of training adaptation were enhanced with twice a day training, the performance of a 1-h time trial undertaken after a 60-min steady-state ride was similar after once daily or twice every second day training programs.