Methodological issues relevant to studies using microarrays and reverse transcription-polymerase chain reaction (RT-PCR) in human aging have rarely been evaluated. Because aging may accentuate biological differences between muscles, we compared transcriptome expression patterns, targeted messenger RNA (mRNA) abundance, strength, and muscle fiber type in the right and left legs of older adults. Muscle biopsies were taken from each Vastus lateralis in eight older (71 +/- 2 years) men, and isometric strength was determined. Samples were analyzed using an Affymetrix gene array, ATPase histochemistry, and RT-PCR for mRNA species involved in metabolism, apoptosis, vascular growth, and antioxidant status. Microarray analysis found that 31 of 5499 genes (0.6%) were significantly different between legs (negative log of the p value [NLOGP] >/= 2.0, but fold < 1.5), with only one gene, jumonji domain containing 1C (JMJD1C), being significantly different by >/= 1.50-fold. None of the mRNA species, or muscle fiber type, size, or strength, was different between legs. These findings are important for the design and analysis of studies using muscle data in older adults.