The present study investigated the factors associated with anemia and micronutrient deficiencies in a cross-sectional analysis conducted with 150 children aged 11 to 14 months attending at basic health centers in Rio Branco, Acre. Venous blood samples were obtained to assess the occurrence of anemia and deficiencies of iron (ID), vitamin A (VAD), and B12 (VB12D). Multiple Poisson regression models were used to identify factors associated with anemia. Anemia, ID, VAD and B12D were observed in 23%, 76%, 18% and 20% of children, respectively. The factors associated with anemia were: do not be only child, living in households without access to cable TV or internet, stunting, late introduction of the complementary feeding (more than 240 days), VAD, VB12D, and current evidence of infection (plasma CRP > 5 mg/L). There was a lower prevalence of anemia among children with birth weight > 3,500 g. Overall, 82% of the study children had at least one of the micronutrient deficiencies (ID, VAD and VB12D). Actions with emphasis on timely and healthy feeding practices, better management of morbidities and supplementation with other micronutrients should be focused on the improvement of child care services at primary health care in this county.