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Molecular typing systems have provided invaluable information for tracking infectious agents through the food chain. These tools have been essential for understanding the epidemiology of gastrointestinal infectious diseases, therefore providing essential and evidence-based information for appropriate interventions and preventative measures. Two such molecular typing techniques based on the polymerase chain reaction (PCR) that have been applied to the epidemiology of foodborne pathogens are, amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) analysis. Campylobacter is responsible for one of the most common bacteria foodborne gastrointestinal infections affecting humans, especially in developed countries. The object of this paper is to apply AFLP and RFLP analysis of the flagellin (flaA) gene to 18 isolates of Campylobacter jejuni from human sporadic cases in Italy. Results of these analyses were compared to the phenotypes of these isolates based on biotyping and antimicrobial resistance determinations. All isolates were typable by the four methods. The RFLP procedure was performed with DdeI and HinfI enzymes, and 12 and 8 distinct profiles respectively were recognised. AFLP analysis was more discriminatory, and recognised 16 different profiles. Results from AFLP were reproducible and applicable for definitive characterisation of C. jejuni isolated from different outbreaks. PCR-RFLP of the flaA gene represents a useful tool only to compare isolates within a single outbreak.