Objective: To investigate the differences of using enzymatic hydrolysis and acid hydrolysis for identification and quantification of isoflavone aglycones from biomatrices. Methods: β-glucuronidase/sulfatase isolated from Helix pomatia for routine enzymatic hydrolysis or 6N HCl was used to release glucuronide and sulfate conjugates in the serum, urine and tissue samples. Profiles of soy isoflavones after enzymatic hydrolysis or acid hydrolysis in several tissues of rat fed with diets containing soy protein isolate were also compared using LC/MS and HPLC-ECD. Results: Acid hydrolysis released more aglycone than enzymatic digestion ( P ＜0.05) in liver tissue. The total genistein, daidzein and other metabolites were 20％ to 60％ lower in samples from enzymatic hydrolysis than in acid hydrolysis. Conclusion: These results indicated that unknown factors in tissues reduced the enzymatic hydrolytic efficiency for releasing isoflavone aglycones even in optimized condition. This would underestimate isoflavone tissue concentrations up to 60％.