The aim of this paper is to optimize and validate a high performance liquid chromatography (HPLC) method for separation and quantification of five isoflavones. A statistical central composite design was used to separate all peaks. These multivariate procedures were efficient in determining the optimal separation condition using resolution, capacity factor, asymmetry and number of theoretical plates. [...] The effective separation of the examined compounds was applied on a Develosil RP Aqueous AR 5 RP-30 column with a gradient mobile phase system and a DAD detector. The isolation and preconcentration of the isoflavones from urine and plasma samples were conducted by means of the solid-phase extraction (SPE). For optimize SPE conditions various sorbents were tested. Furthermore, high recoveries and good relative standard deviations were obtained when the samples were passed through the Oasis HLB column. The developed method was validated and successfully applied for determination of isoflavones in urine and plasma.