We develop a perturbation theory for the Benjamin-Ono (BO) equation. This p
erturbation theory is based on the inverse scattering transform for the BO
equation, which was originally developed by Fokas and Ablowitz and recently
refined by Kaup and Matsuno. We find the expressions for the variations of
the scattering data with respect to the potential, as well as the dual exp
ression for the variation of the potential in terms of the variations; of t
he scattering data. This allows us to introduce the squared eigenfunctions
for the BO equation, whose completeness and orthogonality in both x- and la
mbda-spaces we also establish. We consider the two most important applicati
ons of the developed machinery. First, we present an explicit first-order s
olution of the BO equation driven by a small perturbation. Second, we intro
duce the Poisson bracket and a set of the canonical action-angle variables
for the BO equation, and thus demonstrate its complete integrability as a H
amiltonian dynamical system.