Real exchange rate is one of the factors as its deviation from the equilibrium values ,affect the performance of macro economical variables .In this paper the effect of real exchange rate misalignment on account of the balance of payments during the period 1976 to 2010 are examined. The model which was introduced in this article in order to estimate the misalignment of real exchange rate is the basic model of Edwards. The considered variables in this paper in order to determine the real exchange rate are; Oil incomes, government costs in the services department and buying the non-exchangeable goods, import tariffs, term of trade rate and index of depending on the degree of economic. The period in this study is from 1976 to 2010. Experimental results show that, among the variables affecting Misalignment, variable costs, the most significant impact on the real exchange rate and this variable can impact substantially on the deviation of the real exchange rate from its equilibrium value. The estimation results of Iran's balance of payments account model by the index of real exchange rate misalignment shows that this index had the negative effect on the balance of payments account and results into a deficient in this account.