Duck rearing is well suited to coastal and lowland areas in Bangladesh. It is an important component of sustainable livelihood strategies for poor rural communities as an additional source of household income. An epidemiological study was conducted during January 2005-June 2006 on 379 households in Chatkhil of the Noakhali District, Bangladesh which were using the recently devised "Bangladesh duck model". The overall objective of the study was to identify factors that significantly contributed to mortality and constrained productivity and to generate sufficient knowledge to enable establishment of a disease surveillance system for household ducks. The overall mortality was 15.0% in Chatkhil, with predation causing a significantly higher mortality compared with diseases (p < 0.001). Common diseases were duck plague and duck cholera. Morbid ducks frequently displayed signs associated with diseases affecting the nervous and digestive systems. Haemorrhagic lesions in various organs and white multiple foci on the liver were frequently observed in dead ducks. Epidemiological analysis with a shared frailty model that accounted for clustering of data by farm was used to estimate the association between survival time and risk factors. The overall mortality rate due to disease was significantly lower in vaccinated than in non-vaccinated ducks in all zones except zone 2 (p < 0.001). Only vaccinated ducks survived in zone 1. In conclusion, duck mortality and untimely sale of ducks appeared to be important constraints for household duck production in Chatkhil. Vaccination against duck plague appears to be an effective preventive strategy in reducing the level of associated duck mortality. A successful network was established amongst farmers and the surveillance team through which dead ducks, with accompanying information, were readily obtained for analysis. Therefore, there is an opportunity for establishing a long-term disease surveillance programme for rural ducks in Chatkhil of the Noakhali District of Bangladesh.