The second stage of sampling involved selecting households. In each sample point, 105 households were selected by applying a systematic random sampling technique. This way, a total of 102,060 households were selected. Out of 105 sampled households, ten households in each sample point were selected using a systematic random sampling procedure to conduct interviews for the Long Household and the Women's Questionnaires. Any ever-married woman aged 12-49 years who was a usual resident of the household or a visitor in the household who stayed there the night before the survey was eligible for interview.

The Short Household Questionnaire was administered in 92,340 households to list all the usual members and visitors. Likewise, the Long Household Questionnaire was used in the 9,720 households where the Women's Questionnaire was also administered. In addition to some basic information collected on characteristics like age, sex, marital status, education, and relationship to the head of the household of each person listed, another purpose of the two household questionnaires was to record births and deaths that occurred since January 2003 and, for verbal autopsies, to identify any death of child under age 5 since January 2005 and any death to a woman age 12-49 since January 2003a.

In addition, the Long Household Questionnaire collected more details, e.g., current school attendance, survivorship status of parents of children under age 18, and the registration status of each person. It also identified eligible ever-married women age 12-49 for interview with the Women's Questionnaire. The Long Household Questionnaire also collected information regarding various characteristics of the dwelling unit, such as the source of water; type of toilet facilities; type of cooking fuel; materials used for the floor, roof, and walls of the house; ownership status of various durable goods; ownership of agricultural land; ownership of livestock/farm animals/poultry; and ownership and use of mosquito nets.