Objective To provide an overview of the household dietary diversity score and the food consumption score, two indicators used for food security assessment and surveillance, and compare their performance in food security assessments in three countries. Design Cross-sectional cluster sampling design using an interview-administered structured questionnaire on household food security, including household-level food group consumption measured over 1 d and 7 d. Setting Survey data are from Burkina Faso, Lao People's Democratic Republic (Lao PDR) and northern Uganda. Subjects Households in Burkina Faso (n 3640), Lao PDR (n 3913) and northern Uganda (n 1956). Results Spearman's correlation coefficients between the scores were 0·73 in Burkina Faso, 0·65 in Lao PDR and 0·53 in northern Uganda. Prevalence-adjusted kappa coefficients showed substantial strength of agreement in two countries. The proportion of agreement between the two scores ranged from 85 % in Lao PDR to 65 % in northern Uganda. Dietary profiles based on food group consumption using score tertiles were comparable. Rankings of the most food-insecure areas within a country corresponded well in northern Uganda and Burkina Faso but not in Lao PDR. Both indicators showed moderate correlations with other proxy measures of food security. Conclusions The comparative study highlights the similarities and differences between the food consumption and household dietary diversity scores. Similar classification of the most food-insecure areas within sub-national levels was obtained. The choice of indicator for food security assessment and surveillance will vary depending on user needs.