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We analize instanton generated superpotentials for three dimensional N=2supersymmetric gauge theories obtained by compactifying on S^1 N=1 fourdimensional theories. In the N_f=1 case, we find that the vacua in thedecompactification limit is given by the singular points of the Coulomb branchof the N=2 four dimensional theory (we also consider the massive case). Thedecompactification limit of the superpotential for pure gauge theories withoutchiral matter is interpreted in terms of `t Hooft's fractional instantonamplitudes.Comment: Latex file. 11 pages. Typos corrected. Section on QCD has been  rewritten, clarifying some points, and a reference has been added. Final  version to appear at Int. Jour. Mod. Phys.

M and F Theory Instantons, N = 1 Supersymmetry and Fractional Topological Charge