One of the ancient methods for the generation of bacterial mutants was to insert the composite transposable elements (e.g. Tn10) flanked by desired gene sequences, into the bacterial chromosome. This mechanism of DNA integrating into a chromosome can sometimes not only lead to the creation of desired mutants but also induced other recombination event within the chromosome. Several studies have reported alterations such as deletion, insertion, inversion and both deletion/inversion in the bacterial chromosome due to the insertion of composite transposable elements. In this study it has been found that a Tn10 mutagenesis event not only leads to the inactivation of desired gene (∆aorA), and consequential deletion of other genes upstream of aroA and insertion of IS10, also has resulted in a large-scale chromosomal rearrangement in the Salmonella Typhimurium chromosome. This rearrangement consists of exchange of genetic material between the 10 minute and the 19 minute on a circular chromosomal map (approximately 440 kbps), possibly due to crossover between the two regions. Results from this study are the first evidence of such a large scale rearrangement in the bacterial genome due to the insertion of transposable elements.