Global transcript abundance profiling is a powerful systems biology tool for mapping alterations in phenotype only when careful consideration of the physiological context is maintained. Herein we present the first robust global transcriptome analysis of human skeletal muscle (vastus lateralis) in type 2 diabetes from 118 subjects (type 2 diabetes (n=45), impaired glucose tolerance (n=26) and normal glucose tolerance (n=47)). The study and analysis was approved by the appropriate ethics committees and performed according to the Declaration of Helsinki. Patients were free from diabetic treatment for 1 week prior to assessment. RNA was isolated as previously described (Timmons et al., 2007) profiled on the Affymetrix™ platform covering >47,000 mRNA sequences. We also utilized the TaqMan microRNA (miRNA) real-time qPCR method, to determine the expression of the muscle specific microRNAs (miR-1, miR-133a and miR-206). Comprehensive microarray data analysis (SAM, GSEA, PCA) demonstrated that the global type 2 diabetes muscle transcriptome is invariant with respect to controls. Furthermore, the expression of the mitochondrial OXPHOS gene-set was identical between groups. Profiling of the muscle specific non-coding RNAs, however, demonstrated substantial modulation of these post-transcriptional RNA molecules. In type 2 diabetes patients, miR-133a expression was reduced (unpaired t-test) by a robust 5-fold (p<0.001) and miR-206 (p=0.04) was reduced by 2-fold. Northern analysis demonstrated that only mature miRNA was readily detectable for miR-133a. Importantly, miR-133a expression correlated (pearson) with both short (fasting glucose R2=0.37, p<0.001) and longer term (hbA1c R2=0.29, p<0.001) indices of impaired insulin action. Transcript abundance from the genomic loci of miR-133a demonstrated that primary precursor miRNA (pri-miRNA) production in vivo varies distinctly between the co-located miR-133a and miR-1 genes, yet are unchanged with respect to metabolic status, suggesting that maturation of miR-133a is substantially altered in type 2 diabetes. Thus, contrary to recent claims (relying on smaller, less well controlled patient groups ((Mootha et al., 2003; Patti et al., 2003)) we find that the type 2 diabetes skeletal muscle transcriptome is not characterized by reduced OXPHOS gene expression, while it would appear that inhibition of miRNA molecule production may be a post-transcriptional disease mechanism for altering muscle phenotype in human type 2 diabetes