A retrospective study was performed to assess the mortality rates and clinical signs in commercial and backyard chickens naturally infected with the highly pathogenic avian influenza (HPAI) H5N1 virus in Bangladesh. All of the 33 commercial and 25 backyard farms, recorded during the first wave of HPAI outbreaks (January to November 2007) in Bangladesh, were enrolled in this study. The farm profile data, stock information and major clinical signs recognised by the farmers and/or farm attendants, were collected through a prototype questionnaire. The investigating veterinarians' retrospective appraisals of the clinical signs were recorded by interview. After the clinical onset, the incidence rates of mortality in breeder, commercial broiler, commercial layer and backyard chickens were, respectively: 0.0215, 0.0341, 0.0179 and 0.0703 per chicken-day at risk. The four major clinical signs observed were cyanotic combs and wattles, oedema of the head and face, drowsiness and huddling and ecchymotic discoloration of the leg shanks. The first sign (cyanotic combs and wattles) was equally observed in chickens from commercial and backyard farms (p = 0.44) but the second (oedema of the head and face) was more common in backyard farms (p = 0.03).