Differentiation in the spore-forming bacterium Bacillus subtilis is governed by the sequential activation of five sporulation-specific transcription factors. The early mother-cell-specific transcription factor, sigma(E), directs the transcription of many genes that contribute to the formation of mature, dormant spores. In this study, DNA microarrays were used to identify genes belonging to the sigma(E) regulon. In total, 171 genes were found to be under the control of sigma(E). Of these, 101 genes had not previously been described as being sigma(E) dependent. Disruption of some of the previously unknown genes (ydcC, yhaL, yhbH, yjaV and yqfD) resulted in a defect in sporulation.