To assess dietary isoflavone intake between population and hospital outpatient controls and examine if cancer risks estimated for isoflavone using hospital outpatient controls would be different from those using population controls. Three parallel case-control studies on leukemia, breast, and colorectal cancers in China in 2009–2010 were conducted, using population and hospital outpatient controls to separately match 560 incident cases at a 1:1 ratio. A validated food frequency questionnaire was administered by face-to-face interview. Conditional logistic regression analysis was used to estimate odds ratios (ORs) and 95% confidence intervals (CIs). The 2 control groups had closely similar distributions of dietary isoflavone intake. Risk estimates for breast cancers were adjusted ORs (95% CI) of 0.39 (0.23–0.66) and 0.31 (0.18–0.55) for daidzein, 0.35 (0.20–0.61) and 0.28 (0.16–0.52) for genistein, 0.66 (0.41–1.08) and 0.53 (0.32–0.88) for glycitein, and 0.53 (0.33–0.85) and 0.43 (0.26–0.71) for total isoflavone using hospital outpatient and population controls respectively. The study found that hospital outpatient controls were comparable to population controls in measured dietary intake of isoflavone in the Chinese hospital setting.