Biocompatibility studies of percutanous implants in animal models usually involve numerous lethal biopsies for subsequent morphometric analysis of the implant-tissue interface. A common drawback of the study protocol is the restriction of the analysis to one nal time point. In this study optical coherence tomography (OCT) was used to visualize and enable quantication of the local skin anatomy in the vicinity of a percutaneous implant in an animal model using hairless mice. Non invasive in vivo optical biopsies were taken on predetermined time points after implantation and ex vivo in situ at the day of noticeable in ammation. The custom made Fourier-domain OCT system was programmed for imaging with dierent scanning schemes. A spoke-pattern of 72 cross-sectional scans which was centred at the midpoint of the circular shaped implants was acquired and worked best for the in-vivo situation. Motion-artefact-free three-dimensional tomograms were obtained from the implant site be- fore excision and preparation for histology. Morphometric parameters such as epithelial downgrowth, distance to normal growth and tissue thickness were extracted from the images with a simple segmentation algorithm. Qualitatively, the OCT B-Scans are in good agreement with histological sections. Therefore, OCT can provide additional valuable information about the implant-tissue interface at freely selectable time points before the lethal biopsy. Locally conned quantitative assessments of tissue-implant interaction for in vivo postoperative monitoring can be carried out.