Endoscopy guided probe-based optical biopsy is a new method for detecting sites for tissue biopsy. These sites need to be re-targeted precisely and accurately in subsequent images of the same endoscopy session for treatment or for visual guidance of surgical instruments. A new system for re-targeting biopsy sites and for characterising analytically their uncertainty is presented. It makes use of epipolar lines derived from multiple endoscopic views of the same site. It was tested on real patient data acquired during colonoscopy and gastroscopy. Gold standards of the biopsy site were obtained by Argon Plasma Coagulation tattooing. Re-targeting precision and accuracy were better than 0.8mm which is sufficient for most clinical endoscopic applications.