A single round of indoor residual spraying (IRS) using lambda-cyhalothrin was implemented in a district of Uganda with moderate transmission intensity in 2007. Individual patient data were collected from one health facility within the district 8 months before and 16 months after IRS. There was a consistent decrease in the proportion of patients diagnosed with clinical malaria after IRS for patients < 5 and > 5 years of age (52% versus 26%, P < 0.001 and 36% versus 23%, P < 0.001, respectively). There was a large decrease in the proportion of positive blood smears in the first 4 months after IRS for patients < 5 (47% versus 14%, P < 0.001) and > 5 (26% versus 9%, P < 0.001) years of age, but this effect waned over the subsequent 12 months. IRS was effective in reducing malaria morbidity, but this was not sustained beyond 1 year for the proportion of blood smears read as positive.