The molecular orbital semi-empirical method PM3 was employed to calculate a set of molecular properties (variables or descriptors) of 21 flavonoid compounds with anti-HIV activity. The correlation between biological activity and structural properties was obtained by using the multiple linear regression and partial least squares methods. The model obtained showed not only statistical significance but also predictive ability. The significant molecular descriptors related to the compounds with anti-HIV activity were: electronegativity (χ) and the charges on atoms C3 and C7 (Q3 and Q7, respectively). These variables led to a physical explanation of electronic molecular property contributions to HIV inhibitory potency.