Salmonella enterica serovars Enteritidis and Typhimurium are the serotypes most frequently isolated from human cases. Traditional surveillance systems, based on serological characterisation and epidemiology, are not able to identify these common strains that cause outbreaks in humans. Innovative techniques are therefore necessary to accurately characterise these serotypes and hence accelerate the identification of the primary sources. Within a larger study, the goal of which was to develop an active surveillance system for outbreaks of food-borne diseases, characterisation of 42 Salmonella strains was performed using molecular techniques (pulsed field gel electrophoresis [PFGE] and random amplified polymorphic DNA [RAPD]), together with the Kirby-Bauer antibiotic assay. Results showed that both techniques were unable to satisfactorily characterise the Enteritidis serotype, while only PFGE identified the Typhimurium serotype.