This paper examines the relationship between structural equation modeling and the balanced scorecard in a health care institution. Using financial and non-financial data taken from the social-medical establishment, the paper propose a rational construction of Balanced Scorecard by choosing the right indicators for the right axes. This choice is made by implementing the Partial Least Squares (PLS) in our model. In addition, the scheme gives us the cause-and-effect chain, the one described by Kaplan and Norton as : measures of organizational learning and growth - measures of internal business processes - measures of the customer perspective - financial measures. We will observe that is a health care institution the cause-and-effect chain will change as the primordial goal for a medical-social establishment is not maximizing profitability, but maximizing patient satisfaction. At the end of our article we will proceed to a comparison between two SEM methods : Covariance Based Method (CBM) and Partial Least Squares (PLS).