Abstract Background The food group intake patterns of low income Hispanic and African American preschool children are not well documented. The aim of this study was to perform a food group intake analysis of low income minority preschool children and evaluate how macronutrient and micronutrient intake compares to Dietary Reference Intakes (DRI). Methods A cross sectional study design using three-day food diaries analyzed by dietary analysis software (Nutrient Database System for Research) was used. Children were recruited from well-child clinics at Children’s Healthcare of Atlanta at Hughes Spalding and North Dekalb Grady Satellite Clinic, Atlanta, GA. Low-income, African American and Hispanic preschool age children (n = 291) were enrolled. A total of 105 completed and returned the 3-day food diaries. Chi-squared tests were used to assess demographic variables. The mean percentage of intake per day of specific food groups and sub-groups were obtained (servings of given food group/total daily servings). Food intake data and proportion of children meeting DRIs for macro- and micronutrients were stratified by race/ethnicity, nutritional status, and caloric intake, and were compared using t-tests. Regression models controlling for age, BMI and sex were obtained to assess the effect of total caloric intake upon the proportional intake of each studied food group. Results The mean age of African American children was 2.24 ± 1.07 years and Hispanic children 2.84 ± 1.12 years. African Americans consumed more kcal/kg/day than Hispanics (124.7 ± 51 vs. 96.9 ± 33, p < 0.05). Hispanics consumed more fruits (22.0 ± 10.7% vs. 14.7 ± 13.7%, p < 0.05), while African Americans consumed more grains (25.7 ± 7.8% vs. 18.1 ± 6.4%, p < 0.05), meats (20.7 ± 9.0% vs. 15.4 ± 6.1%, p < 0.05), fats (9.8 ± 5.4% vs. 7.0 ± 5.8%, p < 0.05), sweet drinks (58.7 ± 17.1% vs. 41.3 ± 14.8%, p < 0.05) and low-fat dairy products (39.5 ± 19.3% vs. 28.9 ± 12.6%, p < 0.05). Among Hispanics, the proportional intake of fruits, fats and grains varied by total caloric intake, while no difference by total caloric intake was found for the dietary patterns of African Americans. Micronutrient intake also differed significantly between African American and Hispanic children. Conclusions Food group intake patterns among low-income children differ by ethnic group. There is a need for more research to guide program design and target nutritional interventions for this population.