In Salmonella enterica serovar Typhimurium, retron reverse transcriptase (rrtT), which is part of St 85 retron, is quite ubiquitous and is located in the thdF -yidY intergenic region. In this study, we showed that rrtT is relatively unstable in multidrug resistant, Salmonella genomic island 1 (SGI 1) positive strains. Out of 365 field strains, 55 were free of retron. In 54 of the rrtT negative strains, the excision must have occurred by the same mechanism in which the rrtT together with five other genes was excised. Altogether 8164 bp was missing in the chromosome of the rrtT negative strains. Since the deletion happened exactly between the right inverted repeat of IS 6100 and inside the yieE gene, we propose that intramolecular transposition of IS 6100 followed by homologous recombination was responsible for the excision. Excision of retron together with the right end of SGI 1 may also result in its stabilisation in the Salmonella typhimurium genome. Experimental deletion of rrtT resulted in an accelerated course of infection in orally infected mice. Since the retron excision occurred exclusively in multidrug resistant S. typhimurium, it cannot be excluded that such strains may increase their virulence in the future.