The first years of life are the most dynamic period for childhood growth. There are limited data available on growth patterns of infants and children living in rural Latin America. The aim of this study was to describe the growth patterns from birth to 5years in children living in a rural District of tropical coastal Ecuador using data from a birth cohort of 2404 neonates. We hypothesize that there would be growth differences according to ethnicity and sex. Evaluations were conducted at birth or until 2weeks of age and at 7, 13, 24, 36 and 60months during clinic and home visits. Individual growth trajectories for weight-for-age, height-for-age and weight/height-for-age Z-scores were estimated using multilevel models. Girls were lighter and shorter than boys at birth. However, Afro-Ecuadorian children (versus mestizo or indigenous) were longer/taller and heavier throughout the first 5years of life and had greater mean trajectories for HAZ and WAZ independent of sex and socioeconomic factors. Our data indicate that ethnicity is a determinant of growth trajectories during the first 5years of life independent of socioeconomic factors in a birth cohort conducted in a rural region of Latin America.