Persistent pneumonia associated with H1N1 influenza infection is a rarely reported clinical entity. The authors describe the case of an infant who presented to the emergency department with respiratory distress and a 30-day history of intermittent cough and breathing difficulty. Low grade gastro-oesophageal reflux (GER) was a possible cause for the patient's persistent lower respiratory tract symptoms. However, despite appropriate and adequate therapy for GER, his symptoms persisted and he worsened a week after admission. A search for causes of persistent pneumonia showed positive results for H1N1 virus and isolated IgA deficiency. IgA deficiency in an infant with H1N1 infection has not been previously reported. Inability to mount an adequate local immune response due to deficiency of the antibody could have led to the persistence of symptoms in this case. Screening of family members for the source of infection revealed that the mother was positive for the virus. The authors report this case to highlight the need to rule out underlying IgA deficiency in children with an atypical course of H1N1 pneumonia.