The feasibility of using Fourier transform infrared spectroscopy (FTIR) to detect heat induced conformational rearrangements of proteins, protein-protein and protein-lipid interactions was studied with accelerated shelf-life protocols. Ultra-high temperature treated whole (WM) and skim milk (SM) were stored at 20, 30, 40 and 50 °C for 28 days. The changes leading to increased sedimentation in SM and WM at higher temperatures (≥40 °C) were observed during first 14 days of the storage period. Milk samples stored at 40 and 50 °C showed marked changes in the bands corresponding to conformations of milk lipids and formation of intermolecular β sheet of proteins, indicating protein-lipid interactions and aggregation. Dried sediment contained fat confirming protein-lipid participation in the sedimentation. FTIR was also able to detect changes that led to increased sedimentation in SM at temperatures lower than 40 °C, but only after 28 days.