A child's diet is an important determinant of growth and development. Because of this, the accurate assessment of dietary intake in young children remains a challenge. A systematic search of studies validating FFQ methodologies in children 12 to 36 months of age was completed. English-language articles published until March 2016 were searched using three electronic databases (MEDLINE, EMBASE and CINAHL). Quality assessment of the identified studies was carried out using The Reduced Summary Score and EURopean micronutrient RECommendations Aligned (EURRECA) scoring system. Seventeen studies were included and categorised according to whether they reflected long-term (≥7 d) or short-term (<7 d) intake, or used a biomarker. A total score for each micronutrient was calculated from the mean of the correlation coefficients weighted by the study quality score. At least three validation studies per micronutrient were required for inclusion. Fifteen studies (83 %) that considered validity of the FFQ in assessing nutrient intakes had quality scores from 2·5 to 6·0. Of those, ten (67 %) studies found FFQ to have good correlations in assessing dietary intake (>0·4). Of the nutrients with three or more studies available, FFQ validated using a reference method reflecting short-term intake had a good weighted correlation for Ca (0·51), and acceptable weighted correlations for vitamin C (0·31) and Fe (0·33). Semi-quantitative FFQ were shown to be valid and reproducible when estimating dietary intakes at a group level, and are an acceptable instruments for estimating intakes of Ca, vitamin C and Fe in children 12 to 36 months of age.