Using a flow cytometry-based technique for detecting beta-galactosidase, lacZ fusions have been used to study the pattern of gene expression exhibited by stationary phase cultures of Bacillus subtilis that have initiated the developmental pathway of spore formation. We have found that within such cultures there exist two distinct cell types : one that has induced the developmental program of gene expression and one that has not. This heterogeneity among transcriptional states is shown to be established early during the stationary phase and plays a significant role in influencing later stationary phase events. Additionally, when this technique is used to study gene expression in mutants that display altered patterns of gene expression, we are able to conclude that the cellular apparatus responsible for sensing and transducing stationary phase developmental signals represents a bottleneck that controls the expression of certain early stationary phase genes. These findings provide a demonstration of the utility of single cell measurements of gene expression and indicate that unless culture heterogeneity is properly taken into account, standard measurements of gene expression may not provide information suitable for the analysis of events occurring at the cellular level.