We compared the applicability of an enhanced chemiluminescent (ECL) method for using gene probes with that of radioactive probes to identify enterotoxigenic Escherichia coli (ETEC) in stools of Bangladeshi children with diarrhoea. Colony blots of E. coli isolates were hybridized using both [alpha-32P]-dCTP labelled and fluorescein-11-dUTP labelled polynucleotide and oligonucleotide gene probes for heat-labile enterotoxin (LT), and heat-stable enterotoxin (ST). Analysis of 1,620 isolates obtained from 540 patients gave similar results by both radioactive and chemiluminescent probes. The ECL method was faster than the radioactive method. Both polynucleotide and oligonucleotide probes could be used by the ECL method. Hybridization and detection by the ECL method appeared to be a convenient alternative to radioactive probes for screening E. coli isolates for ETEC.