This paper examines the effects of capital structure on performance of quoted non-financial firms in Nigeria between 1996 and 2012. The study employed both the first and second generation econometrics method of panel unit root test, principal component analysis, and Generalized Method of Moments. Using return on assets, returns on equity, price earnings ratio, Tobin's Q, and constructed Performance Index as measures of firm performance and debt ratio as a measure of capital structure. Our result showed that capital structure has a negative and significant relationship with firm performance. The study concluded that the agency costs of the non-financial firms under the Nigerian Stock Exchange are very high and these lead to negative performance.