The objective of this study was to compare the presence of the Arkansas (Ark) and Massachusetts (Mass) serotypes of infectious bronchitis virus (IBV) in the tracheas and cecal tonsils of commercial broilers after vaccination at 1 day of age by coarse spray. When given as a single serotype vaccine, the Mass strain was detected by reverse transcriptase-polymerase chain reaction (RT-PCR)-restriction fragment length polymorphism (RFLP) only in the tracheas, whereas the Ark strain was detected in both the tracheas and cecal tonsils. By in situ hybridization, the Mass and Ark nucleocapsid (Nc) genes were detected only at 7 days in the tracheas. When both strains were given in the mixed vaccine, the Mass strain was more consistently detected by RT-PCR-RFLP in the tracheas and cecal tonsils at early stages of infection (up to 14 days) and the Arkansas strain was more consistently detected at late stages of infection (21 and 28 days). By in situ hybridization, the IBV Nc gene was more consistently detected in the trachea at early stages of infection (7, 14, and 21 days) and in the cecal tonsils at late stages of infection (21, 28, and 35 days). In general, the Mass strain was more frequently recovered from the tracheal and cecal tonsil tissues at earlier stages of infection and the Ark strain was recovered at later stages of infection.