We assess trends in children's nutritional status in Equatorial Guinea, a country in socioeconomic transition. Nationally representative samples were conducted in 1997, at the start of the economic take off, and again in 2004. Children aged 0–60 months were included in the surveys (N =436, 552). Both surveys included a sociodemographic, dietary and health questionnaire, and anthropometric measurements from which height-for-age (HAZ); weight-for-age (WAZ) and weight-for-height (WHZ) Z-scores were calculated. Between 1997 and 2004, the prevalence of child overweight for all children increased from 21.8% to 31.7%, especially in urban areas (from 18.2% to 29.4%, p =0.01). Stunting prevalence among children ≥2 years old decreased (from 57.9% to 45.3%, p <0.02), but for all age groups remained very high (34.7% overall, 46.5% rural and 28.5% urban in 2004). The economic take off in Equatorial Guinea appeared to coincide with substantial increases in the prevalence of child overweight whereas the prevalence of stunting decreased even if it remained high. The results suggest that the country is undergoing a nutrition transition and acquiring the concomitant double burden of under and over nutrition.