The recent development of fused-core technology in HPLC columns is enabling faster and highly efficient separations. This technology was evaluated for the development of an fast analysis method for the most relevant soy isoflavones. A step-by-step strategy was used to optimize temperature (25-50 °C), flow rate (1.2-2.7 mL/min), mobile phase composition and equilibration time (1-5 min). Optimized conditions provided a method for the separation of all isoflavones in less than 5.8 min and total analysis time (sample-to-sample) of 11.5 min. Evaluation of chromatographic performance revealed excellent reproducibility, resolution, selectivity, peak symmetry and low limits of detection and quantification levels. The use of a fused-core column allows highly efficient, sensitive, accurate and reproducible determination of isoflavones with an outstanding sample throughout and resolution. The developed method was validated with different soy samples with a total isoflavone concentration ranging from 1941.53 to 2460.84 μg g-1 with the predominant isoflavones being isoflavone glucosides and malonyl derivatives. © 2010 Elsevier B.V.