Gene expression in microbes can be detected with an oligonucleotide-based DNA macroar-ray. The DNA macroarray is composed of short (22-24-mer) oligonucleotide probes immobilized onto a nylon membrane via polyinosine tails. An indirect high-density labeling method was used to effectively incorporate biotin into the nucleic acids. The hybridization signals were detected with a chemiluminescence-based method and digitized with a desktop scanner. The utility of this protocol was demonstrated by profiling the expression of 375 metabolically related genes in Lactococcus lactis ssp. lactis IL1403 during heat, acid, and osmotic stresses. The macroarray accurately detects known stress responses in lactococci. Additionally, expression profile changes of a commercial starter during cheddar cheese ripening can also be profiled.