Validation of a food frequency questionnaire (FFQ) utilising a short-term measurement method is challenging when the reference method does not accurately reflect the usual food intake. In addition, food group intake that is not consumed on daily basis is more critical when episodically consumed foods are related and compared. To overcome these challenges, several statistical approaches have been developed to determine usual food intake distributions. The Multiple Source Method (MSM) can calculate the usual food intake by combining the frequency questions of an FFQ with the short-term food intake amount data. In this study, we applied the MSM to estimate the usual food group intake and evaluate the validity of an FFQ with a group of 333 Korean children (aged 3-6 y) who completed two 24-hour recalls (24HR) and one FFQ in 2010. After adjusting the data using the MSM procedure, the true rate of non-consumption for all food groups was less than 1% except for the beans group. The median Spearman correlation coefficients against FFQ of the mean of 2-d 24HRs data and the MSM-adjusted data were 0.20 (range: 0.11 to 0.40) and 0.35 (range: 0.14 to 0.60), respectively. The weighted kappa values against FFQ ranged from 0.08 to 0.25 for the mean of 2-d 24HRs data and from 0.10 to 0.41 for the MSM-adjusted data. For most food groups, the MSM-adjusted data showed relatively stronger correlations against FFQ than raw 2-d 24HRs data, from 0.03 (beverages) to 0.34 (mushrooms). The results of this study indicated that the application of the MSM, which was a better estimate of the usual intake, could be worth considering in FFQ validation studies among Korean children.