Bordetella hinzii isolated from the trachea and lungs of a laboratory mouse with a respiratory infection was identified based on its phenotypic and genetic traits. The mouse showed sneezing with a chattering sound but without nasal discharge, and histopathologic examination revealed rhinitis, tracheitis, and bronchopneumonia. The isolate was a gram-negative, oxidase- and catalase-positive, short rod-shaped organism that produced alkali from malonate. The results of biochemical identification, an alkali production test from malonate, and partial sequence analysis of the 16S rRNA gene (1523 bp) were consistent with those reported previously for B. hinzii. The isolate induced sneezing in ICR mice and sneezing and slight to severe dyspnea in NOD-SCID mice after experimental infection. Histopathologic examination revealed catarrhal rhinitis and bronchopneumonia in both strains of mice and interstitial pneumonia in NOD-SCID mice. In light of these findings, B. hinzii was deemed to be a novel causative agent of respiratory disease in mice. This report describes the first isolation of B. hinzii from a mouse and confirms the organism's pathogenicity in mice.