We performed a cross-sectional study to compare the intake of energy, macronutrients, fiber, sodium and iron and the anthropometric status of infants and toddlers living in North (Milano) and South Italy (Catania). Nutrient intake was evaluated using a 7-day weighed food record. Out of 400 planned children aged 6 to 36 months, 390 (98%) were recruited, 189 in Milano and 201 in Catania. The mean (standard deviation) age was 17 (9) months in Milano and 17 (10) months in Catania. Anthropometry, energy intake and macronutrient intake were similar in Milano and Catania. However, iron intake was 27% lower and fiber intake 16% higher in Milano than in Catania. Despite normal anthropometry and energy intake, in the pooled sample there was a high intake of proteins, simple carbohydrates, saturated fats and sodium, and a low intake of iron and fiber compared to Italian reference values. This is the first study to report the macro- and micro-nutrient intake of children aged <12 months using the 7-day weighed food record and one of the very few studies that have employed such reference method in children from the general population.