Nutrition program planners often need information on the relative burden of malnutrition in different communities, or administrative units, to decide where best to invest limited available resources. National nutrition surveys, however, rarely provide precise, representative findings at a finer level than that of large, subnational regions. The school height census is an alternative, low-cost approach that does provide disaggregated data on growth retardation at the local level. This study assessed the reliability and validity of the school height census for small-area targeting of nutrition interventions in Honduras. Reliability was assessed by examining the stability of small-area estimates of mean height-for-age Z-score over five consecutive years from 1993 to 1997. Validity was assessed by comparing municipality-level mean height-for-age Z-score in the 2001 school height census with the same parameter estimated in an anthropometric survey of children < 5 y old conducted in representative samples in 70 municipalities 3-7 mo earlier. The study found that stable estimates of mean height-for-age Z-score could be obtained at the level of municipalities or larger (intraclass correlation coefficients > or = 0.85). The school height census estimates of mean height-for-age Z-score at the municipality level were also valid, with the reference criterion the survey results for children > or = 1 y of age (Spearman's rank correlation = 0.74). School height censuses cannot provide reliable estimates of levels of growth retardation in individual schools. Wider use of school height censuses could make it much easier to identify communities that might benefit from targeted nutrition interventions.