OBJECTIVE:To identify and compare the sociodemographic determinants of stunting, wasting and overweight among infants of urban and rural areas in the Ecuadorian highlands. DESIGN:Cross-sectional study. SETTING:Nabon (rural) and Cuenca (urban) cantons, Azuay Province, Ecuador. SUBJECTS:A total of 703 children aged 0-24 months and their caregivers (227 rural and 476 urban) recruited during the period from June to September 2008. RESULTS:Stunting prevalence was significantly higher in the rural area (37·4 % v. 17·7 %; P < 0·001) while wasting (7·1 %) and overweight (17·1 %) prevalence were more similar between areas. Determinants of stunting for the pooled sample were male gender (OR = 1·43; 95 % CI 1·06, 1·92; P = 0·02), preterm delivery (OR = 1·65; 95 % CI 1·14, 2·38; P = 0·008), child's age (OR = 1·04; 95 % CI 1·01, 1·07; P = 0·011), maternal education (OR = 0·95; 95 % CI 0·92, 0·99; P = 0·025) and facility-based delivery (OR = 0·57; 95 % CI 0·45, 0·74; P < 0·001). The latter was also a determinant of overweight (OR = 0·39; 95 % CI 0·25, 0·62; P < 0·001). Rural determinants of stunting were maternal height (OR = 0·004; 95 % CI 0·00004, 0·39; P = 0·018), diarrhoea prevalence (OR = 2·18; 95 % CI 1·13, 4·21; P = 0·02), socio-economic status (OR = 0·79; 95 % CI 0·64, 0·98; P = 0·030) and child's age (OR = 1·07; 95 % CI 1·02, 1·11; P = 0·005). Urban determinants were: maternal BMI for stunting (OR = 0·91; 95 % CI 0·84, 0·99; P = 0·027), cough prevalence (OR = 0·57; 95 % CI 0·34, 0·96; P = 0·036) and facility-based delivery (OR = 0·25; 95 % CI 0·09, 0·73; P = 0·011) for overweight, and hygiene for wasting (OR = 0·57; 95 % CI 0·36, 0·89; P = 0·013). CONCLUSIONS:Infant malnutrition was associated with different sociodemographic determinants between urban and rural areas in the Ecuadorian highlands, a finding which contributes to prioritize the determinants to be assessed in nutritional interventions.