  We examine the effects of instantons in four dimensional N=1 supersymmetric
gauge theory by including D0-branes in type IIA brane constructions. We examine
instanton generated superpotentials in supersymmetric QCD and find that they
are due to a repulsive force between D4-branes bound to D0-branes ending on NS
5-branes. We study situations where instanton effects break supersymmetry such
as the Intriligator-Thomas-Izawa-Yangagida model and relate this to a IIA brane
construction. We also argue how confinement due to a condensate of fractional
instantons manifests itself in Super Yang-Mills theory using fractional D0
branes, D4 branes, and NS strings.
