Most of our current understanding of brain function and dysfunction has its firm base in what is so elegantly called the 'anatomical substrate', i.e. the anatomical, histological, and histochemical domains within the large knowledge envelope called 'neuroscience' that further includes physiological, pharmacological, neurochemical, behavioral, genetical and clinical domains. This review focuses mainly on the anatomical domain in neuroscience. To a large degree neuroanatomical tract-tracing methods have paved the way in this domain. Over the past few decades, a great number of neuroanatomical tracers have been added to the technical arsenal to fulfill almost any experimental demand. Despite this sophisticated arsenal, the decision which tracer is best suited for a given tracing experiment still represents a difficult choice. Although this review is obviously not intended to provide the last word in the tract-tracing field, we provide a survey of the available tracing methods including some of their roots. We further summarize our experience with neuroanatomical tracers, in an attempt to provide the novice user with some advice to help this person to select the most appropriate criteria to choose a tracer that best applies to a given experimental design.