The value of clearing and staining whole organisms to study vertebrate anatomy is unquestionable. These methods have been developed for over a century leading to protocols to prepare triple-stained specimens to differentiate between bones, cartilage, and nerves. Despite their potential to advance the field of comparative anatomy, nerve-staining methods have been used by a small number of vertebrate systematists in part because of the inconsistently successful preparations. Here, we report on several modifications to the current Sudan black B protocols and propose a new acid-free protocol to differentiate among bone, cartilage, and nerves in whole small vertebrates. This method may also be used to stain solely bone and cartilage by eliminating the nerve-staining steps. The technique herein described is successful for preparing juveniles and adults (including miniatures).