Insertion of polymeric biliary endoprostheses is widely used as a method of palliation of malignant strictures of the biliary tree. Despite the success of this technique, clogging of the stent in a few months is still an existing problem. The aim of the present study has been to investigate the causes of the obstruction, considering both the stent material and the composition of the obstructing deposit. 16 ready-to-implant and 33 occluded retrieved prostheses were analysed by ATR-FTIR spectroscopy. The clogging sludge was recovered and studied by FTIR spectroscopy and pyrolysis derivatisation/gas chromatography/mass spectrometry (Py/GC/MS). The results of the analyses showed that the deposit was mainly formed by proteins, bilirubin, calcium palmitate and bilirubinate, cholesterol and its fatty acids salts. It was found that approximately 50% of the examined ready-to-implant samples were made of ethylene-vinylacetate copolymer (EVA) instead of polyethylene (PE), as was stated in the producer declaration. Moreover, 94% of the retrieved samples were found to be made of EVA indicating that this material is less suitable than PE for this application. All retrieved PE and EVA stents showed a protein-like black layer strongly absorbed on the surface.