Among field isolates of infectious bronchitis virus (IBV) from recent outbreaks, some isolates that were classified into the 4/91 genotype, by analysis of the S1 gene, have been confirmed to be a new variant in Japan. To elucidate the characteristics of these isolates, pathogenicity in chicks and the efficacy of vaccines against this new variant were examined. Severe respiratory symptoms were observed in 4-day-old specific pathogen free chicks inoculated with a 4/91 genotype isolate, either JP/Wakayama/2003 or JP/ Iwate/2005; body weights 3 wk after inoculation were significantly lower than those of chicks inoculated with a 4/91 vaccine strain. These 4/91 isolates were neutralized with serum from birds immunized with 4/91 vaccine. In a challenge-protection test, five groups of chicks were immunized with C78, TM-86w, H120, Kita-1, or 4/91 vaccines and then challenged with JP/Iwate/2005 4 wk after vaccination. A protective effect in the 4/91 and TM-86w vaccine groups was indicated by evaluation of the ciliostasis score of the trachea, the respiratory symptom score, and virus isolation from trachea swab samples after challenge. The results of this study suggested that the 4/91 type of IBV, which is virulent to chicks when compared to vaccine strains, has emerged as a new variant in Japan, and vaccines containing the 4/91 strain or the TM-86w strain could be effective for this variant.