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The December 2004 tsunami in Sumatra, Indonesia, destroyed drinking water infrastructure, placing over 500,000 displaced persons at increased risk of waterborne disease. In June 2005, we assessed the relationship of water handling behaviors to household water quality in three districts: Aceh Besar, Simeulue, and Nias. We surveyed 1,127 households from 21 communities and tested stored drinking water. Factors associated with a reduced likelihood of having contaminated stored drinking water included obtaining water from improved sources (Aceh Besar, adjusted odds ratio (aOR) 0.41, P < 0.01; Simeulue, aOR 0.48, P = 0.02), using chlorine solution (Simeulue, aOR 0.41, P < 0.01), and having free chlorine in stored water (Aceh Besar, aOR 0.42, P < 0.01; Nias, aOR 0.28, P < 0.01). Reported boiling, even among those who could describe correct practice, was not associated with improved water quality. Water source improvement and household water chlorination appear to be useful strategies to improve household stored drinking water quality in post-disaster situations.