We present an improved methodology to estimate the underlying structure of systematic risk in the Mexican Stock Exchange with the use of Principal Component Analysis and Factor Analysis. We consider the estimation of risk factors in an Arbitrage Pricing Theory (APT) framework under a statistical approach, where the systematic risk factors are extracted directly from the observed returns on equities, and there are two differentiated stages, namely, the risk extraction and the risk attribution processes. Our empirical study focuses only on the former; it includes the testing of our models in two versions: returns and returns in excess of the riskless interest rate for weekly and daily databases, and a two-stage methodology for the econometric contrast. First, we extract the underlying systematic risk factors by way of both, the standard linear version of the Principal Component Analysis and the Maximum Likelihood Factor Analysis estimation. Then, we estimate simultaneously, for all the system of equations, the sensitivities to the systematic risk factors (betas) by weighted least squares. Finally, we test the pricing model with the use of an average cross-section methodology via ordinary least squares, corrected by heteroskedasticity and autocorrelation consistent covariances estimation. Our results show that although APT is very sensitive to the extraction technique utilized and to the number of components or factors retained, the evidence found partially supports the APT according to the methodology presented and the sample studied.