  Every countable directed graph generates a Fock space Hilbert space and a
family of partial isometries. These operators also arise from the left regular
representations of free semigroupoids derived from directed graphs. We develop
a structure theory for the weak operator topology closed algebras generated by
these representations, which we call free semigroupoid algebras. We
characterize semisimplicity in terms of the graph and show explicitly in the
case of finite graphs how the Jacobson radical is determined. We provide a
diverse collection of examples including; algebras with free behaviour, and
examples which can be represented as matrix function algebras. We show how
these algebras can be presented and decomposed in terms of amalgamated free
products. We determine the commutant, consider invariant subspaces, obtain a
Beurling theorem for them, conduct an eigenvalue analysis, give an elementary
proof of reflexivity, and discuss hyper-reflexivity. Our main theorem shows the
graph to be a complete unitary invariant for the algebra. This classification
theorem makes use of an analysis of unitarily implemented automorphisms. We
give a graph-theoretic description of when these algebras are partly free, in
the sense that they contain a copy of a free semigroup algebra.
