Purpose: The objective of this study was to assess and investigate the epidemiology of pertussis in infants under 6 months of age. Methods: A prospective study was conducted between October 1, 2011 and April 30, 2013 in CHA Bundang Medical Center, Seongnam, South Korea. Polymerase chain reaction (PCR) or culture was used to detect Bordetella pertussis in nasopharyngeal aspirates from case patients who were hospitalized for acute lower respiratory tract infection (LRTI). In addition, multiplex real-time PCR assays were also performed to detect 6 etiologic viruses, including adenovirus, human metapeumo-virus, influenza virus, parainfluenza virus, respiratory syncytial virus and rhinovirus. Results: Of the 79 enrolled case patients, whose median age was 2 months of age, the most common diagnoses uncovered in this study were acute bronchiolitis (60%) and pneumonia (28%). B. pertussis infection was found in 13 cases (16%), in which 7 (53%) was coinfected with respiratory syncytial virus and 1 (7%) with influenza A virus. Of the 13 patients with B. pertussis infection, 6 (46%) were not vaccinated with the diphtheria, tetanus toxoid, and acellular pertussis vaccine, while 6 (46%) received 1 dose, and 1 (8%) received 2 doses. Conclusion: B. pertussis infection was present in 16% of under 6 month-old infants, who were hospitalized for acute LRTI. Therefore, a nationwide epidemiological surveillance of pertussis, including institutions that cater to infants under 6 months of age is necessary and needed.