A method of marking an orientation of a cut specimen of tissue prior to excision thereof from a body includes steps of disposing a tissue-marking probe in the body adjacent the cut specimen, the tissue-marking probe including a tissue-marking tool configured to selectively mark the cut specimen. A surface of the cut specimen is then marked with the tissue-marking tool such that the orientation of the cut specimen within the body is discernable after the cut specimen is excised from the body. The tissue-marking tool may be configured to selectively bow out of and back into a window defined near a distal tip of the probe and the marking step may include a step of selectively bowing the tissue-marking tool out of the window and following the surface of the cut specimen while rotating the probe. The tissue-marking tool may include an RF cutting tool and the marking step may include a step of coagulating or cauterizing a selected portion of the surface of the cut specimen with the RF cutting tool. Alternatively, the marking step may include a step of delivering dye onto selected portions of the surface of the cut specimen.