The aim of this study was to determine the structural relationships of qnrA1 and other resistance genes in four integrons contained in four clinical isolates of Klebsiella pneumoniae. In the four integrons, the sequences surrounding qnrA1 were similar to those described for pMG252 (accession no. AY070235). The four integrons carried a class 1 integrase gene belonging to the complex class 1 integron. Three of the strains contained an identical integron coding for resistance to beta-lactams, aminoglycosides, chloramphenicol and trimethoprim. The fourth strain contained a different integron coding for resistance to beta-lactams, aminoglycosides and chloramphenicol. Downstream of the last integron, copies of IS6100 and IS26 were present. We describe two new and different integrons containing qnrA1. These integrons code for resistance to different groups of antimicrobial agents from K. pneumoniae clinical strains isolated in the USA.