Abstract Background Cardiovascular diseases (CVD) are amongst the leading causes of death worldwide. Risk factors of CVD develop during childhood and adolescence, and dietary quality has been linked to the development of CVD itself. This study examines the association between dietary patterns and cardiovascular risk in a group of urban and rural Ecuadorian adolescents from different socioeconomic backgrounds. Methods A cross-sectional study was conducted from January 2008 to April 2009 among 606 adolescents from the 8th, 9th and 10th grade in an urban area (Cuenca), and 173 adolescents from a rural area (Nabón) in Ecuador. Data collection involved measuring anthropometric data (weight, height and waist circumference), blood pressure, dietary intake (2-day 24 h recall) and socio-demographic characteristics. Fasting blood lipids and glucose were measured in a subsample of 334 adolescents. Factor analysis was used to identify dietary patterns and linear regression models were used to (i) identify differences in food intake practices according to socioeconomic status and place of residence and (ii) establish relationships between dietary patterns and cardiovascular risk factors. Results Median energy intake was 1851 kcal/day. Overall, fiber, fish and fruit and vegetables were scarcely consumed, while added sugar, refined cereals and processed food were important constituents of the diet. Two dietary patterns emerged, one labelled as “rice-rich non-animal fat pattern” and the other one as “wheat-dense animal-fat pattern”. The first pattern was correlated with a moderate increase in glucose in urban participants, while the second pattern was associated with higher LDL and cholesterol blood levels in rural participants. Conclusions This group of adolescents presented various dietary practices conducive to CVD development. Effective strategies are needed to prevent CVD in the Ecuadorian population by encouraging a balanced diet, which contains less refined cereals, added sugar, and processed food, but has more fruits, vegetables and whole grain cereals.