All countries worldwide are experiencing difficulties in setting maximum residue limits (MRLs) for pesticide residues in food commodities due to prohibitive costs, labor, and other expenses. The Codex Alimentarius (Codex) is actively engaged in revising the classification of food commodities that are grown in small areas; however, setting MRLs for all agricultural commodities has not been effective. Modified food classifications for groups of agricultural commodities were established for setting MRLs of pesticides for each food commodity. Codex accepted various countries' opinions that the old food classification of commodities can no longer be applied to the present food classifications; therefore, from 2009, Codex started to revise their food classifications. To set pesticide MRLs for agricultural products grown in small fields, groups of agricultural commodities were subdivided, and new food classifications were used. The food classification revised by Codex made it easy to set up group MRLs. After the Codex food classification was revised, jujube and persimmon, which were previously classified as tropical fruits, were grouped as pome fruits and stone fruits based on the opinion of the Korea Food & Drug Administration (KFDA). In addition, KFDA submitted more comments on the classification of various vegetables. As a result, Korean vegetables were included in the food classification by Codex. The current Codex food classifications in Korea still have not adopted a group-specific subdivision system that is already used in Codex and the US internationally harmonized food classification revisions by Codex might resolve the difficulty of setting up pesticide MRLs for agricultural commodities such as vegetables in Korea. Consequently, food classifications in Korea, which are in harmony with the Codex food classification, will be of great help in setting the group MRLs for the minor crops of Korea.