Tissue banking methods such as brain banking often face a trade-off between morphological and molecular preservation. For example, cryopreservation is preferred for subsequent molecular assays, while fixation by aldehyde crosslinking is commonly used for microscopy. Among aldehyde fixatives, formaldehyde is often considered better for immunohistochemistry, while glutaraldehyde is often considered better for electron microscopy. However, it is unclear whether morphological versus molecular preservation trade-offs reflect fundamental biology or technology limitations. As a window into this discussion, in this narrative review, I evaluate the literature regarding the effects of glutaraldehyde on molecular preservation, with an emphasis on nervous system tissue. Available evidence suggests that crosslinking with glutaraldehyde has minimal direct effects on most molecular features, with a few critical exceptions such as protein conformation. On the other hand, glutaraldehyde fixation frequently fails to retain non-directly crosslinked molecules such as lipid and carbohydrate species during subsequent dehydration steps. Further, as a result of probe diffusion limitations or strong covalent interactions with glutaraldehyde, many molecules can be more difficult to visualize or otherwise measure in tissue fixed with glutaraldehyde. As a practical guide for investigators that are considering using glutaraldehyde, I also point out representative molecular assays that have been performed in tissue fixed with glutaraldehyde, and how this set of assays could be improved and expanded in the future.