Environmental causes of heaves are well described, but the molecular mechanisms of the disease remain unclear. Previous studies have highlighted the implications of variations in gene expression, most using reverse transcription polymerase chain reaction (RT-PCR). This well-known technique limits the number of genes that can be studied in a single assay. Microarray appears to be a valuable tool to by-pass this limitation, but so far there has been no equine-specific microarray available on the market. The present study was performed to determine whether a human microarray could be used to study gene expression in nucleated cells originating from peripheral blood and bronchoalveolar lavage fluid (BALF) in heaves-affected horses. With a four-fold cut-off, a total of 46 candidates were identified with differentially regulated genes between heaves-affected horses and controls. A real-time quantitative RT-PCR (RT-QPCR) conducted on a selection of genes, determined on the basis of previous publications, was used to validate the microarray results. The microarray failed to detect the presence of interleukin (IL)-1beta and IL-8 mRNA in the nucleated cells from BALF otherwise confirmed by real-time RT-QPCR. Although some candidate genes have been identified using this method, a complete expression profile of genes related to heaves could not be obtained with the use of the human microarray.