He used two instruments primarily in the study of anatomy, his scalpel to "remove the flesh and define structures" and his pen and ink to "add to paper and define structures". His sketches often clearly reveal the bone structures, muscle layers and nerves that he discovered in the course of dissection.
He noted down his observations in notebooks and from studying the human body via dissection he came to understand how muscles worked and how the various organs worked within the body. In his book Anatomical Studies (published in 1510) he describes his work as a "thinking hand".
From discovering the Divine proportion in man to making stunning illustrations of anatomy Leonardo left us a legacy. His drawings enabled people to understand the inside of the body more clearly as other artists would discover.
If you have time I strongly recomend you take a look at the weblink "Artwork by Leonardo Da Vinci" (under Resources) and see his work for yourself.