The purpose of this study was the output and set up of the milk array, a dedicated array designed to investigate the expression levels of many genes involved in cow mammary gland inflammation and milk production regulation. First, a new targeted genes panel was selected. Successively, the microarray reliability was examined by yellow and dye swap experiments using the normal and mastitic mammary gland samples from the same cow. The sensitivity and reliability were evaluated using different amounts of the same mastitic mammary gland RNA: a good linear regression (R (2) = 0.758) was obtained also using only 3 μg of RNA. We used both reverse transcriptase RT-qPCR and the microarray to analyze 100 bovine genes (96 known to be involved in inflammation and milk production regulation and four housekeeping genes) in pooled total RNA isolated from tissue samples. All genes were detectable by RT-qPCR and microarray: a good mean correlation coefficient over all samples of 0.885 showed that both methods were similarly well suited to analyze gene expression in these samples. This report describes the development of small DNA microarray of fully defined genes suitable for analysis of expression of many genes involved in cow mammary gland inflammation and milk production regulation; this platform will prove useful as diagnostic tool prototype to perform a more in-depth analysis of the milk quality and mammary glands health status.