In this study we sequenced and analysed the fimH and fimA genes of 24 avian pathogenic Escherichia coli (APEC) isolates, in order to investigate their possible conserved nature. Additional parameters (serotype, presence of aerobactin receptor, expression of F1 pili and virulence for chickens) were investigated to look for correlations with the obtained sequences. The sequence analysis demonstrated that FimH is highly conserved among all investigated APEC strains (>99% homology), whereas the major subunit FimA is less conserved, presenting 6 variable regions distributed along the protein. A hydrophilicity analysis suggested several variable domains of FimA to be potential epitopes. We were able to classify the investigated strains into three main groups, on the basis of the amino-acid sequences of the variable regions. This grouping was consistent throughout all variable regions and was independent of serotype, leading to an improved classification of the F1 pili. No correlation was found between the fimH and fimA sequences and the following parameters: avian species, organ of isolation, serotype, presence of aerobactin receptor and virulence for chickens. This study elucidated the molecular structure and the degree of conservation of FimH and FimA among various avian pathogenic E. coli strains.