The transcriptional co-activator PGC-1α is recognized as the master regulator of mitochondrial biogenesis. However, recently a novel isoform, PGC-1α4 that specifically regulates muscle hypertrophy was discovered. Since stimulation of mTORC1 activity is tightly coupled to hypertrophy, we hypothesized that activation of this pathway would upregulate PGC-1α4. Eight male subjects performed heavy resistance exercise (10 x 8-12 repetitions at ~75% of 1RM in leg press) on four different occasions, ingesting in random order a solution containing essential amino acids (EAA), branched-chain amino acids (BCAA), leucine or flavored water (placebo) during and after the exercise. Biopsies were taken from the vastus lateralis muscle before and immediately after exercise, as well as following 90 and 180 min of recovery. Signaling through mTORC1, as reflected in S6K1 phosphorylation, was stimulated to a greater extent by the EAA and BCAA than the leucine or placebo supplements. Unexpectedly, intake of EAA or BCAA attenuated the stimulatory effect of exercise on PGC-1α4 expression by ~50% (from a 10-fold to 5-fold increase with BCAA and EAA, P<0.05) 3 h after exercise, whereas intake of leucine alone did not reduce this response. The 60% increase (P<0.05) in the level of PGC-1α1 mRNA 90 min after exercise was uninfluenced by amino acid intake. Muscle glycogen levels were reduced and AMPKα2 activity and phosphorylation of p38 MAPK enhanced to the same extent with all four supplements. In conclusion, induction of PGC-1α4 does not appear to regulate the nutritional (BCAA or EAA) mediated activation of mTORC1 in human muscle.