Background. Microarrays can measure simultaneously the expression of thousands of genes and identify subtle changes in expression between different biological states. In our lab a novel two-step subtractive strategy was settled in order to enrich for genes expressed at low levels in skeletal muscle. Methods. Using this cDNA collection we have developed a dedicated muscle-specific microarray composed of 2,700 sequences corresponding to the 400-500 most 3′-terminal region of muscle transcripts. Results. The expression profile of limb-girdle dystrophy type 2B was analysed with our array. Conclusions. We found approximately 3% differentially expressed genes, mostly involved in muscle contraction and immune response.