Fowl adenovirus (FAdV) associated diseases have emerged as major viral diseases in all types of poultry around the globe. These diseases have been re-emerging as outbreaks throughout Pakistan in recent years, therefore, the purpose of the current study was to conduct molecular epidemiology of Fowl Adenovirus in commercial poultry depending upon different variables. The study is based on n=675 farm samples (each sample represents organ collection of 5 birds per farm) from commercial poultry around division Faisalabad, Pakistan during years 2018- 2020. Type of chicken affected, age groups, shed types, seasons and regions were assumed as risk factors associated with the prevalence of FAdVs which were analyzed using non-parametric tests. For molecular studies, liver tissues were subjected to polymerase chain reaction (PCR) by targeting hexon gene. The current study showed higher prevalence in layer type chicken among commercial chicken types, younger birds showed higher FAdV prevalence due to possible vertical transmission and higher prevalence of FAdV infection was observed in commercial poultry kept in semi-environment control sheds due to inconsistent control over the biosecurity and internal environment of the shed. This study also reported shed type and season to be significantly associated (P<0.05) with risk of FAdV infection.