A detailed description of the structure of two-ended arc-transitive digraphs is given. It is also shown that several sets of conditions, involving such concepts as Property Z, local quasi-primitivity and prime out-valency, imply that an arc-transitive digraph must be highly-arc-transitive. These are then applied to give a complete classification of two-ended highly-arc-transitive digraphs with prime in- and out-valencies.