In histological processing, the loss of a small biopsies can prevent diagnosis by the pathologist. Appropriate specimen marking dyes are helpful, but those sold for the purpose have trade-secret components. The purpose of this study is to find suitable dyes with known chemistry to improve the visibility of small specimens. Samples of various organs, including stomach, lung, nasopharynx, small intestine and sentinel lymph nodes, were labeled with Rose red D-FR (CI 282855, Direct red 227), Blue 2RL (CI 24315, Direct blue 80), and Purple D-5BL (CI 29120, Direct violet 66). Clinical pathologists evaluated the dyeing capability and determined any interference of the marking dyes with diagnosis of stained sections. Direct red 227, Direct blue 80, and Direct violet 66 all increased the visibility of small specimens, without interfering with hematoxylin & eosin (HE) staining or immunohistochemistry. All three dyes can therefore be recommended for marking small specimens such as biopsies.