A rapid fowl adenovirus (FAdV) classification method based on a 30-bp sequence of the hexon loop (L1) was developed using the pyrosequencing technique. FAdV identification is relevant for epidemiological studies and for the adoption of a correct strategy where vaccination is to be used for the control of the disease. FAdV typing is usually performed using polymerase chain reaction coupled with either conventional DNA sequencing or restriction enzyme analysis; however, both methods can be time consuming and/or very expensive to be used as a routine tool. In the present study, polymerase chain reaction and subsequent pyrosequence analysis of the variable hexon L1 region were assessed in order to rapidly differentiate FAdV species. Forty-nine FAdV samples (22 reference strains and 27 field isolates) were tested and the results were compared with those obtained by conventional DNA sequencing. The results clearly demonstrated that pyrosequence analysis provides a new approach for a rapid differentiation and classification of the FAdV species that is faster, more cost-effective and easier to interpret than other techniques commonly used.