This paper demonstrates the feasibility of using the penalty function method to estimate parameters that are subject to a set of functional constraints in covariance structure analysis. Both types of inequality and equality constraints are studied. The approaches of maximum likelihood and generalized least squares estimation are considered. A modified Scoring algorithm and a modified Gauss-Newton algorithm are implemented to produce the appropriate constrained estimates. The methodology is illustrated by its applications to Heywood cases in confirmatory factor analysis, quasi-Weiner simplex model, and multitrait-multimethod matrix analysis.