Mutations in PINK1 have been linked to Parkinson’s disease and Drosophila pink1 mutants obtained severe mitochondrial defects. In this study we profiled the gene expression from the PINK1 locus in metabolic syndrome. The PINK1 locus includes PINK1, DDOST (encoding the AGE-R1 receptor) and naPINK1 (a cis-encoded natural antisense to PINK1). We utilized quantitative real-time PCR to examine the gene expression in skeletal muscle and adipose tissue from a human cohort consisting of four groups matched for age, gender and smoking status: non-obese (n=12) or obese (n=14), normal glucose tolerant (n=13) or type 2 diabetes subjects (n=14). Considering the confounding effect that exercise-inducible genes may have in metabolic disease, we included two control studies, measuring the PINK1 locus genes before and after inactivity or activity in healthy volunteers. In parallel, we examined the expression of PGC-1α being an established diabetes related gene. We demonstrate that following 5 weeks of inactivity (n=6, healthy volunteers), PINK1 was decreased in skeletal muscle while naPINK1 was increased. Consistently, the opposite regulation pattern was observed following 6 weeks of activity. The expression of DDOST remained unaltered in both studies. In contrast, all PINK1 locus genes were down-regulated in skeletal muscle of type 2 diabetes. Importantly, skeletal muscle PINK1 expression correlated with diabetes status (fasting glucose and HbA1c) and siRNA knockdown of PINK1 did impair basal glucose metabolism. Surprisingly, the gene expression of the diabetes candidate gene, PGC-1α, was neither consistently reduced nor related to measures of metabolic syndromes. In adipose tissue, PINK1 expression co-varied with mtDNA encoded mRNA suggesting the operation of the Pink1-Parkin-OXPHOS pathway found previously in Drosophila. In conclusion, PINK1 expression is regulated by physical activity in muscle, while expression of the whole genomic locus is uniquely down regulated in metabolic disease. Whether down-regulation of PINK1 is part of a type 2 diabetes causative pathway or is a secondary effect of hyperglycemia remains to be investigated.