BackgroundInsecticide-based tools remain critical for controlling vector-borne diseases in Uganda. Securing public support from targeted populations for such tools is an important component in sustaining their long-run effectiveness. Yet little quantitative evidence is available on the perceived benefits and costs of vector control programmes among targeted households.MethodsA survey was administered to a clustered random sample of 612 households in Gulu and Oyam districts of northern Uganda during a period of very high malaria transmission and following a pilot indoor residual spray (IRS) programme. A discrete choice experiment was conducted within the survey, in which respondents indicated their preferences for different IRS programmes relative to money compensation in a series of experimentally controlled, hypothetical choice sets. The data were analysed using conditional logit regression models to estimate respondents’ willingness to accept (WTA) some amount of money compensation in lieu of foregone malaria risk reductions. Latent class models were used to analyse whether respondent characteristics predicted WTA.ResultsAverage WTA is estimated at $8.94 annually for a 10 % reduction in malaria risk, and additional co-benefits of IRS were estimated to be worth on average $54–$56 (depending on insecticide type) per round of IRS. Significant heterogeneity is observed: Four in five household heads in northern Uganda have high valuations for IRS programmes, while the remaining 20 % experience costly side effects of IRS (valued at between $2 and $3 per round). Statistically significant predictors of belonging to the high-value group include respondent gender, mean age of household members, participation in previous IRS, basic knowledge of mosquito reproduction, and the number of mosquito nets owned. Proxies for household income and wealth are not found to be statistically significant predictors of WTA.ConclusionsThis study suggests that the majority of people in areas of high malaria transmission like northern Uganda place a high value on vector control programmes using IRS. However, there is significant heterogeneity in terms of the perceived side effects (positive and negative). This has implications for sustaining public support for these programmes in the long-term.Electronic supplementary materialThe online version of this article (doi:10.1186/s40249-016-0190-1) contains supplementary material, which is available to authorized users.