Abstract Microarrays traditionally have been used to assay the transcript expression of coding regions of genes. Here, we use Escherichia coli oligonucleotide microarrays to assay transcript expression of both open reading frames (ORFs) and intergenic regions. We then use hidden Markov models to analyse this expression data and estimate transcription boundaries of genes. This approach allows us to identify 5′ untranslated regions (5′ UTRs) of transcripts as well as genes that are likely to be operon members. The operon elements we identify correspond to documented operons with 99% specificity and 63% sensitivity. Similarly we find that our 5′ UTR results accurately coincide with experimentally verified promoter regions for most genes. Contact: [email protected] Keywords: untranslated regions; operons; intergenic; microarrays; Escherichia coli. *To whom correspondence should be addressed.