We have developed and reported several micro-spikes for minimally invasive biopsy. This paper presents a diagnosis protocol for micro-spike biopsy using paraffin-based tissue collecting tool. Using the proposed tissue collecting tool, which has a negative micro-spike structure in a porous chamber, the biopsied tissue in a micro-spike is effectively detached. The proposed diagnosis protocol prevents the loss of tissues in a paraffin embedding and sectioning process. Hence, it is compatible with conventional histopathology without additional reagents and processes. The gastro-intestinal tissue of a pig is biopsied in an in vivo environment, and then it is detached from a micro-spike using the paraffin-based tissue collecting tool. A histopathological photomicrograph of the detached tissue is acquired with the proposed diagnosis protocol. The acquired image offers clinical quality. This result shows that the paraffin-based tissue collecting tool is applicable to the medical practice.