Objective: The present study aimed to systematically analyse the complete lipid profile of the in situ pellicle in comparison to saliva. For the first time, the modern sensitive methods GC-EI/MS and HPLC MS/MS were to be used for this purpose. Design: Bovine enamel slabs were exposed to the oral cavity of 12 subjects by customized splints (3 min, 30 min or 120 min). Afterwards, the pellicle samples were obtained and further investigated in vitro. Additionally, corresponding unstimulated saliva samples were collected. GC-EI/MS was performed to qualitatively and quantitatively determine all fatty acids contained in the investigated samples. The individual lipid classes of phospholipids, triacylglycerols, glycolipids, cholesterol and cholesterol esters were analysed qualitatively by HPLC MS/MS. Results: A characteristic fatty acid profile of the in situ pellicle was proven. Furthermore, triacylglycerols with the major fatty acids 16:0, 18:0, 18:1, 18:2, and phospholipids were detected as integral components in the pellicle. There were four groups of phospholipids: Lyso-phosphatidylcholines, phosphatidylcholines, phosphatidylethanol-amines, and phosphatidylinositols. Differences between saliva and pellicle were evident in the composition of the fatty acid- and the phospholipid profile. Glycolipids, cholesterol and cholesterol esters could neither be detected in pellicle- nor in saliva samples. Conclusion: The lipid profiles of the in situ pellicle and saliva were successfully characterised. Differences in the phospholipid and fatty acid composition between pellicle and saliva indicate a selective pellicle formation process. The results provide an important reference and core data for further investigation of the complex surface interactions in the oral cavity, especially concerning hydrophobic substances.