Five hundred and seventy-three clinical submissions with fowl adenovirus (FAdV) involvement were examined to investigate the association of different types of FAdV with clinical problems related to FAdV infection. Samples were received from 2000 to 2006 and originated from seven Canadian provinces. Four hundred and eighty-seven submissions were inclusion body hepatitis (IBH) related, while 86 were not IBH related. Viruses isolated from 287 samples were further analysed by hexon gene loop 1 sequencing. Twenty-seven genotyped FAdVs were from Alberta, 20 from British Columbia, 16 from Manitoba, one from Nova Scotia, 82 from Ontario, 64 from Quebec and 77 from Saskatchewan. Two hundred and forty-six analysed FAdVs were from IBH cases, confirmed by liver histopathology, by FAdV isolation from the liver, or both. Based on hexon gene loop 1 sequencing analysis, FAdVs associated with IBH outbreaks were genetically related to FAdV02 (nine isolates, 99.4%), FAdV08a (100 isolates, 99.4% to 100%) and FAdV11 (98 isolates, 99.4% to 100%). Thirty-nine viruses were 93.7% to 94.3% identical to FAdV07 strain x11a, but the genetic and immunogenic properties of this strain require further investigation. In IBH cases, the co-infection rates for infectious bursal disease virus, infectious bronchitis virus, reoviruses and Newcastle disease virus were 3.47%, 1.04%, 6.25% and 0.69%, respectively. Forty-one genotyped FAdVs were from "non-IBH" cases. Viruses isolated from non-IBH cases consisted of 22 FAdV01, 15 FAdV11, two FAdV08a and one each of FAdV02 and FAdV04 viruses. Co-infection rates in non-IBH submissions were 50.00% for infectious bursal disease virus, 40.70% for infectious bronchitis virus, 27.91% for reoviruses and 1.16% for Newcastle disease virus.