We develop a gauge-invariant formalism to describe metric perturbations in
five-dimensional brane-world theories. In particular, this formalism applie
s to models originating from heterotic hi theory. We introduce a generalize
d longitudinal gauge for scalar perturbations. In this gauge, we derive the
five-dimensional evolution equations for scalar perturbations as well as t
he most general structure of the scalar brane stress-energy tensor. As an a
pplication, we discuss some aspects of the evolution of fluctuations on the
brane. Moreover, we show how the five-dimensional formalism can be matched
to the known four-dimensional one in the limit where an effective four-dim
ensional description is appropriate.