Inflammation in skeletal muscle is a consistent feature of Lyme borreliosis, both in the human disease and experimental models. This study had two goals: to evaluate the expression of selected pro-inflammatory and chemokine genes in skeletal muscle in the Rhesus model of Lyme disease, and to identify unexpected cytokine genes involved in Lyme myositis. Two different techniques for measuring cytokine messenger RNA (mRNA) levels were used to achieve these goals: gene expression microarrays and. real-time RT-PCR (Taqman). Muscle from necropsies and biopsies were used, and were obtained from both infected and uninfected non-human primates (NHPs). Although many cytokines were found expressed in muscle tissue, pro-inflammatory cytokines commonly associated with inflammation were not consistently upregulated in infected muscles relative to uninfected muscles. However, B-lymphocyte chemoattractant (BLC), a chemokine implicated in the trafficking of B-cells into tissue, was increased in expression. This study is the first to extensively characterize cytokine gene expression in chronically inflamed tissue in Lyme borreliosis.