The 2007 Kenya Malaria Indicator Survey was the first of its kind in Kenya. The population of interest was women ages 15-49 years and children under the age of 5 years living malaria endemic areas. The survey covered 63 of the 69 administrative districts (as of the 1999 census) and excluded: Nairobi Province; Kiambu, Nyandarua and Nyeri districts in Central Province; Meru Central district in Eastern Province; and Laikipia district in Rift Valley Province.

A two-stage cluster sampling design and the National Sample Survey and Evaluation Program (NASSEP IV) sample frame was used. Clusters were selected by probability proportional to size. A total of 1,800 clusters were created, including 1,360 rural and 560 urban. A total of 7,200 households were selected from these clusters.

Data collection included both household and women's questionnaires, and was conducted using personal digital assistants (PDAs). Blood tests for hemoglobin and malaria parasites were collected from children under 5.