Outbreaks of salpingitis and peritonitis in poultry cause major economic losses due to a high mortality,reduced egg-production and culling. The aim of the present study was to characterized in detail lesions associated with increased mortality in layers due to avian pathogenic E. coli (APEC), and to investigate the population structure of E. coli involved which is important for selection of optimal treatment and prophylactic strategies. Among 322 layers received from eight farms with increased mortality due to E. coli, three lesion types were observed: sepsis like lesions (I), chronic salpingitis and peritonitis (II), and chronic salpingitis and peritonitis associated with sepsis-like lesions (III). One hundred isolates of E. coli obtained in pure culture from the different lesion types were selected for genetic characterization. Six out of 10 submissions (two farms with two submissions) were considered clonal as defined by more than 85% of the typed isolates of E. coli belonging to the same sequence-type (ST). B2 was the most prevalent phylogroup including the clonal complex of ST95. The most important virulence genes of E. coli were demonstrated from both clonal and non-clonal outbreaks, and major differences as to phylogeny and virulence genes were not observed between the lesion types. Cannibalism and other predisposing factors were more often observed during polyclonal outbreaks. A new pathotype SPEC of APEC is suggested based upon lesions and 34 route of infection, high similarity of virulence genes, including plasmid associated genes, and high frequency of ST95 and other isolates belonging to phylogroup B2. This phylogroup is also the most prevalent among human urinary infections, the human equivalent to avian salpingitis, indicating that common source of the two types of infection might exsist.