Background
Indoor residual spraying (IRS) is known to reduce malaria transmission. In northern Uganda, a high endemic area, IRS has been implemented since 2006. Limited data however, exists on the effect of IRS on the malaria burden. This study sought to assess the effect of IRS on malaria morbidity in the high intensity area of northern Uganda. Retrospective routine data from ten health facilities in three districts which had received at least five rounds of IRS in northern Uganda was analysed. The primary outcome of interest was malaria morbidity, measured by the slide positivity rate (SPR). Descriptive statistics were used to describe the malaria morbidity stratified by age and sex. The average change in the malaria morbidity, measured by the SPR was assessed according to time, measured as calendar months. A fixed-effects linear regression model was used which included a polynomial function of time and controlled for malaria seasonality and variations between districts/facilities.

Results
The total out-patient department attendance in the ten health facilities for the study period was 2,779,246, of which 736,034 (26.5%) malaria cases were diagnosed with 374,826 (50.9%) cases of under 5 years and an overall SPR of 37.5%. The percentage point (p.p.) changes in SPR according to time measured as calendar months following IRS, revealed a decreasing trend in malaria morbidity in the first 3 months following each round of IRS. The highest percentage point decrease in the SPR was observed in the second month following IRS (9.5 p.p., CI −17.85 to −1.16, p = 0.026), among patients above 5 years. The SPR decline however waned by the fourth month following IRS, with an increase in the SPR of 8.4 p.p. at district level by the sixth month, p = 0.510.

Conclusion
The study results show that IRS was associated with a significant reduction in malaria morbidity in northern Uganda in the first 3 months following IRS. The malaria reduction however waned by the fourth month following IRS.