An eight month old boy presented with a subacute febrile illness and radiological evidence of multifocal cavitatory consolidations in the lungs. He continued to worsen despite multiple oral and intravenous antibiotics. Preterminally, he developed respiratory distress, hepatosplenomegaly, bicytopenia, and hepatic dysfunction. Investigation for cause of persistent pneumonia resulted in a diagnosis of chronic granulomatous disease on the basis of Dihydrorhodamine assay and genetic analysis. Postmortem blood culture grew Burkholderia cenocepacia. Autopsy revealed necrotizing granulomatous inflammation with massive necrosis and abscesses in bilateral lungs. No organism could be identified by traditional stains on autopsy. Conventional PCR targeting 16S ribosomal DNA yielded Nocardia pseudobrasiliensis. In conclusion, an unusual course of pneumonia warrants invasive investigations for isolation of underlying organism, which not only provides guidance to choice of antimicrobials but also provides clue to an underlying disease.