Tackling childhood malnutrition is a global health priority. A key indicator is the estimated prevalence of malnutrition, measured by nutrition surveys. Most aspects of survey design are standardised, but data ‘cleaning criteria’ are not. These aim to exclude extreme values which may represent measurement or data-entry errors. The effect of different cleaning criteria on malnutrition prevalence estimates was unknown. We applied five commonly used data cleaning criteria (WHO 2006; EPI-Info; WHO 1995 fixed; WHO 1995 flexible; SMART) to 21 national Demographic and Health Survey datasets. These included a total of 163,228 children, aged 6–59 months. We focused on wasting (low weight-for-height), a key indicator for treatment programmes. Choice of cleaning criteria had a marked effect: SMART were least inclusive, resulting in the lowest reported malnutrition prevalence, while WHO 2006 were most inclusive, resulting in the highest. Across the 21 countries, the proportion of records excluded was 3 to 5 times greater when using SMART compared to WHO 2006 criteria, resulting in differences in the estimated prevalence of total wasting of between 0.5 and 3.8%, and differences in severe wasting of 0.4–3.9%. The magnitude of difference was associated with the standard deviation of the survey sample, a statistic that can reflect both population heterogeneity and data quality. Using these results to estimate case-loads for treatment programmes resulted in large differences for all countries. Wasting prevalence and caseload estimations are strongly influenced by choice of cleaning criterion. Because key policy and programming decisions depend on these statistics, variations in analytical practice could lead to inconsistent and potentially inappropriate implementation of malnutrition treatment programmes. We therefore call for mandatory reporting of cleaning criteria use so that results can be compared and interpreted appropriately. International consensus is urgently needed regarding choice of criteria to improve the comparability of nutrition survey data.