In this study, the interaction of green tea flavonoids with milk proteins and the effect of heat treatment on the flavonoid-protein binding were examined. Reverse-phase high-performance liquid chromatography (RP- HPLC) analysis revealed that the free flavonoids decreased in the presence of milk proteins and a binding ratio (%) was calculated based on this decrease. Green tea extract (GTE) was added into the milk protein system before and after heat treatment. Three different heat treatment norms were selected (80, 85, 90oC x 10 min). Analyses were carried out in both sodium caseinate and skimmed milk samples to observe the possible effect of milk serum proteins on the interaction. The binding ratio between flavonoids and proteins was found to be higher in the samples where GTE was added before heat treatment than in the samples where GTE was added after heat treatment in both the skimmed milk and sodium caseinate systems. Results of the PSH index and protein partition also demonstrated that heat treatment must be applied after the addition of GTE to improve the amount of GTE binding to milk proteins. From food science and technology points of view, flavonoids are important compounds that influence both the quality and stability of food products and can be used for manufacturing of novel milk products. This study presents a holistic approach to examine the usage of functional compounds such a green tea flavonoids in dairy products.