Introduction: Geographical conditions may be linked with food insecurity and growth retardation in young children. This research assessed household food insecurity status and undernutrition in different geographical areas. Methods: A cross-sectional study was conducted in four different types of geographical areas: coastal, limestone, agricultural and municipality, which were purposely selected in East Java Province. The samples were households with children aged below 5 years. A total of 736 households that fulfilled the inclusion criteria were recruited. Household food security was assessed using the Household Food Security Supplement Measure (US-HFSSM) adapted for developing countries. Nutritional status of children was determined and classified according to World Health Organization Growth Standard (2006). Results: Prevalence and severity of household food insecurity differed significantly among the different geographical areas. Almost half (44.8%) of the households were categorised as “food insecure without hunger”. Prevalence of “hunger” was highest in coastal (7.2%) and limestone areas (5.3%). Highest prevalence of stunting was in coastal areas (11.6%), whereas highest prevalence of wasting (6.2%) and underweight (8.9%) were in limestone areas. Prevalence of undernutrition was relatively low among children living in municipalities. The differences in the distribution of undernutrition of young children and household food insecurity status were statistically associated with the types of geographical areas. Conclusion: Prevalence of household food insecurity differed according to the types of geographical areas in East Java. Prevalence of household food insecurity and young child undernutrition were greater for households in the coastal and limestone areas, compared to those in the agricultural and municipality areas.