Microvirgula aerodenitrificans is a denitrifying Gram-negative organism first described by Patureau et al. in 1998 (D. Patureau et al., Int. J. Syst. Bacteriol. 48:775-782, 1998). The organism has been isolated globally but has never been described as causative of clinical infection. We describe the first human case of bacteremia attributed toM. aerodenitrificans in an infant with Pompe's disease.