Bifidobacterium breve is an effective probiotic agent used in the field of neonatology. Although B.breve has been considered safe, a case of B.breve bacteremia has been reported. The pathogenic mechanism underlying the bacteremia is unknown. Herein, we report a second case of B.breve bacteremia that developed in a neonate with multiple abdominal organ anomalies. Following surgical repair immediately after birth, B.breve treatment was started. After 1week, the infant developed B.breve bacteremia following the onset of adhesive ileus. The bacteremia was thought to have been associated with an intestinal obstruction. A pediatric culture bottle is theoretically unsuitable for incubating B.breve because B.breve is an obligate anaerobic bacterium. It was, however, cultured from pediatric culture bottles in the present case, suggesting that pediatric culture bottles may be useful for procuring B.breve and for determining antimicrobial susceptibility for screening purposes in neonatal patients.