Abstract Background Describing adverse health effects and identifying vulnerable populations during and after a disaster are important aspects of any disaster relief operation. This study aimed to describe the mortality and related risk factors which affected the displaced population over a period of two and a half months after the 2004 Indian Ocean tsunami in an eastern coastal district of Sri Lanka. Methods A cross-sectional household survey was conducted in 13 evacuation camps for internally displaced persons (IDP). Information on all pre-tsunami family members was collected from householders, and all deaths which occurred during the recall period (77 to 80 days starting from the day of the tsunami) were recorded. The distribution of mortality and associated risk factors were analysed. Logistic regression modelling using the generalized estimating equations method was applied in multivariate analysis. Results Overall mortality rate out of 3,533 individuals from 859 households was 12.9% (446 deaths and 11 missing persons). The majority of the deaths occurred during and immediately after the disaster. A higher mortality was observed among females (17.5% vs. 8.2% for males, p p p p p Conclusion A significantly high mortality was observed in women and children among the displaced population in the eastern coastal district of Sri Lanka who were examined by us. Reconstruction activities should take into consideration these changes in population structure.