According to 'Countdown to 2015', more than 114,000 children die each year in Mozambique before reaching their fifth birthday. And is estimated 45% of these deaths is linked to malnutrition. The purpose of this study was to determine the prevalence of chronic malnutrition, acute malnutrition and underweight in children under 2 years of age. A cross-sectional study was made at Cabo Delgado, Niassa and Nampula’s province in Mozambique. Anthropometric measurements (height for age, weight for height and weight for age) were made to 689 children under 2 years age. A team formed by 6 pollsters, 3 controllers and 6 nurses conducted the anthropometric measurements from April to June 2015. The anthropometric indicators used to access the nutritional status were: height-for-age (HA), weight-for-height (WH) and weight-for-age (WA). Measures were expressed in the form of a Z-score, which include: HAZ < −2 (stunting/chronic malnutrition), WHZ < −2 (wasting) and WAZ < −2 (underweight). The total rate of positive cases of malnutrition was: 51.6% stunting (320/619), 9% of wasting (56/613) and 17.9% (119/662) of underweight. Stunting prevalence was especially high among children with 6-11 months old. Stunting prevalence was higher in Niassa (55.7%) compared to Cabo Delgado (50.5%) and Nampula (39.2%).The rate of acute malnutrition was three times higher in rural communities (10%) compared to urban communities (7%). Underweight prevalence was higher in Cabo Delgado (23.8%) compared to Nampula (20.4%) and Niassa (14.4%). Our findings allowed us to draw recommendations to improve the implementation of health programs against malnutrition in these provinces.