This paper begins the development of a theory of what we will call symplectic alternating algebras. They have arisen in the study of 2-Engel groups but seem also to be of interest in their own right. The main part of the paper deals with the challenging classification of some algebras of this kind which arise in the context of 2-Engel groups and give some new information about these groups. The main result is that there are 31 such algebras with dimension 6 over the field of three elements.