Verbal autopsy (VA) aims to estimate a community's mortality experience in the absence of contact with formal registration or health care systems. Application of VA to neonatal deaths is problematic as the agonal phase of a neonatal death tends to be indistinct. This is the first attempt to validate the technique exclusively on newborns who died. Seriously ill neonates (n = 137) were enrolled from the Civil Hospital, Karachi, Pakistan, between 31 October 1993 and 31 July 1994. All died as newborns, and caregivers were interviewed at home 3–230 days later. Surveillance physicians completed case questionnaires in the hospital, and investigator physicians assigned the main and associated causes of death using clinical criteria. Field questionnaires including a verbatim open-ended history, and syndrome modules were completed by a field worker, and investigator physicians again assigned the main and associated causes of death based on three diagnostic methods: verbatim alone, modules alone and verbatim and modules combined. We assessed the validity of VA by comparing field against hospital diagnoses by diagnostic (verbatim vs. modules vs. both) and analytic method (main vs. any diagnosis). VA identified at least one diagnosis accurately in 71% of the newborns. VA underdiagnosed low birthweight and prematurity in the field. Verbatim and modules diagnostic method comparing any field against main hospital diagnoses revealed high sensitivities for too early/too small syndrome (90%) and neonatal tetanus (84%). VA correctly identified some important causes of neonatal death in the field. Assigning multiple diagnoses using both open- and closed-ended questions increases the likelihood of correct ascertainment.