sRNAFinder is a new gene prediction system for systematic identification of noncoding genes in bacteria. Most noncoding RNAs in prokaryotes belong to a class of genes denoted as small RNAs (sRNAs). In the model organism Escherichia coli, over 70 sRNA genes have been identified, and the existence of many more has been hypothesized. While various sources of information have proven useful for prediction of novel sRNA genes, most computational approaches do not take advantage of the disparate sources of data available for identifying these noncoding RNA genes. We present a general probabilistic method for predicting sRNA genes in bacteria. The method, based on a general Markov model, is implemented in the computational tool sRNAFinder. sRNAFinder incorporates heterogeneous data sources for gene prediction, including primary sequence data, transcript expression data from microarray experiments, and conserved RNA structure information as determined from comparative genomics analysis. We demonstrate that sRNAFinder improves upon current tools for identifying small, noncoding genes in bacteria.