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Necrotic enteritis (NE) is an enteric disease of poultry caused mainly by Clostridium (C.) perfringens type A. The disease re-emerged due to increasing restrictions of routine use of antimicrobial growth promoters in poultry farming in Europe and worldwide. The pathogenesis of NE seems to be multifactorial and de-pends on bacterial virulence factors, host-related factors such as stress, and predisposing factors e.g. coc-cidiosis. C. perfringens is supposed to use an arsenal of more than 16 toxins to cause intestinal infections in animals and humans. C. perfringens alpha toxin (CPA) has been considered a major virulence factor for NE but its role is still not clear. Additionally a novel so called Necrotic Enteritis Toxin B-like (NetB toxin) is believed to play a key role in NE pathogenesis. However, the detection of netB-negative strains associated with NE in poultry and netB-positive strains in healthy birds has called its impact into question. Our aim is to determine the prevalence of known virulence elements within C. perfringens strains isolated from healthy and infected chickens from different regions. In addition we use Illumina/Solexa sequencing tech-nology to generate whole genome sequence data for selected strains in order to identify NE strain-specific markers.