Hens were vaccinated during the rearing phase with infectious bronchitis virus (IBV) vaccines commercially available in Australia (Vic S and A3) or left unvaccinated and then challenged with the N1/88 strain of IBV at 30 wk of age. Oviduct and fecal samples were collected at regular intervals after N1/88 challenge. A locked nucleic acid probe-based reverse transcription real-time PCR test was designed and used to detect the IBV strain N1/88 from the oviduct and feces of unvaccinated and vaccinated laying hens. Using a recombinant plasmid standard, the detection limit of the reaction was found to be 100 copies and independent assay runs showed reproducible threshold cycle values. Viral RNA was detected in the oviduct of 12 unvaccinated then challenged hens and viral RNA increased sharply on d 10 and 12 postinfection (p.i.). By contrast, among the hens in the vaccinated group, N1/88 was detectable only in the oviduct of 2 hens at 8 and 12 d p.i. N1/88 challenge. Viral RNA was detected in feces of 2 unvaccinated hens up to 4 wk p.i. and in 1 vaccinated hen up to 3 wk p.i. This shows that rearing phase vaccination lowers the total viral RNA of the strain N1/88, even though this strain shows considerable antigenic and genetic variation from the vaccine strain. This new test will be useful for the rapid identification of the N1/88 strain of IBV from oviduct and fecal samples.