The aim of the present study was to investigate the effect of acute aerobic exercise on the expression of PGC-1α transcript variants in human skeletal muscle. Seven endurance-trained athletes performed a 90-min cycling test (62% of VO2max). At resting state, the levels of N-truncated (NT)-PGC-1α and PGC-1α exon 1a-derived transcripts were significantly higher (>20-fold; P<0.05) than those of PGC-1α exon 1b- and 1c-derived transcripts. Acute exercise did not change the PGC-1α exon 1a-derived expression level, but it did increase the expression level of NT-PGC-1α mRNAs 6-fold, and the expression levels of PGC-1α exon 1b- and 1c-derived mRNAs>200-fold (P<0.05). We conclude that NT-PGC-1α transcript expression in resting muscle and after acute moderate-intensity exercise constituted a significant share of total PGC-1α expression. The exercise led to a higher level of PGC-1α expression from alternative promoters (exon 1b- and 1c-derived mRNA) than from the canonical proximal promoter (exon 1a-derived mRNA).