  In this dissertation we discuss various issues concerning application of the
Dijkgraaf-Vafa (DV) conjecture to the study of supersymmetric gauge theories.
The DV approach is very powerful in that it provides a systematic way of
computing the nonperturbative, often even exact, superpotential of the system,
which was possible only on a case-by-case basis in the more traditional
approach based on holomorphy and symmetry.
  This conjecture has been checked for many nontrivial examples, but the range
of its applicability remained unclear. We give an explicit example, Sp(N)
theory with antisymmetric tensor, which reveals the subtleties in applying the
conjecture. We show that, the superpotential obtained by a straightforward
application of the DV approach starts to disagree with the standard gauge
theory result at N/2+1 loops. The same discrepancy is reproduced in the
generalized Konishi anomaly method.
  In order to look for the physical origin of the discrepancy, we consider the
string theory realization of the gauge theories by Calabi-Yau
compactifications. By closely analyzing the physics that accompanies the
geometric transitions involved, we clarify the prescription regarding when to
include a glueball field as the physical field, and when to not. In particular,
the aforementioned discrepancy is resolved if we follow this prescription and
introduce a glueball field for the "Sp(0)" group.
  Furthermore, we generalize the prescription to include flavors and
demonstrate that the matrix model computations with the generalized
prescription correctly reproduce the gauge theory results.
