Introduction
Quite often disease data are available in aggregated formats mostly to maintain confidentiality. This leads to a misalignment problem when the goal is to analyze risk at a different level of spatial resolution different from the original administrative level where data were available.

Objective
To estimate and map the risk of measles at a sub-region level in Namibia using data obtained at a regional level.

Methods
Using measles data from Namibia for the period 2005–2014, both multi-step and direct approaches were applied to correct for misalignment. Subsequently, ecological Bayesian regression models were fitted and compared.

Results
Results show that the variables standardized birth rate, counts of measles cases for previous year, unemployment rate and proportion of vaccinated children against measles by age 12 months were significant determinants of measles risk. Constituencies having elevated measles risk were identified mostly in the northern corridor with Angola.

Conclusion
We recommend that relevant authorities should make geographical target intervention and redesign prevention and control strategies based on these findings.