One hundred and forty-two Enterobacteriaceae isolates randomly selected from four general hospitals in Nanjing region of China were investigated for antibiotic susceptibility, the presence of integrons and the characterisation of gene cassettes. Eighty-five (59.9%) Enterobacteriaceae strains contained class 1 integrons, and 17 (65.4%) of 26 Shigella contained class 2 integrons. Class 3 integrons were not detected in this study. Restriction fragment length polymorphism (RFLP) and DNA sequencing analysis revealed seven different cassette arrays of class 1 integrons; additionally, four cassette arrays identified in this study were reported for the first time in some species. The genes most commonly found in these class 1 integrons were those for aminoglycoside and trimethoprim resistance. In conclusion, class 1 and 2 integrons were widespread in Enterobacteriaceae and Shigella, respectively, in Nanjing area of China and it was likely that integrons played an important role in antibiotic resistance. Characterisation of cassette arrays of integrons could be a useful epidemiological tool to study the evolution of multidrug resistance and the dissemination of antibiotic resistance genes.