In this work, we analysed 56 clinically failed and retrieved implants by means of scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS) and histological studies. The surface contamination was compared to that of unused control implants and with that of the same implants after cleaning in a basic medium. The surfaces of the unused implants presented considerable contamination. In particular, high levels of carbon were detected. The nature of this C was elucidated by XPS analysis of the lubricant used in the machining process. The same contamination was observed in the retrieved implants. Histological studies were carried out by means of light microscopy. Fibrosis and granulomatous lesions were detected in the tissues. XPS analysis indicated the presence of traces of other elements (Na, Ca, Zn, S, F, etc.) that were not related to impurities in cpTi. We examined a cleaning process in a basic medium that eliminates the organic components of the implant surfaces. The cleaned implants were implanted in the patients and the results were excellent. None of the implants failed in following 7 months.