The role of antioxidative agents in coronary artery disease (CAD) has been investigated, but the analysis of specific flavonols intake in Polish adults requires validated tools. The aim of this study was to estimate the dietary intake of flavonols in CAD patients by creating a food frequency questionnaire (FFQ) dedicated for this purpose in Polish adults. The FFQ included 140 products from 12 food groups. The study involved 103 adult respondents (43 CAD patients and 60 healthy controls). Mean daily intakes of total flavonols, quercetin, kaempferol, myricetin and isorhamnetin were calculated as absolute values and quartiles. Mean daily intakes of 12 main food categories and 27 subcategories were calculated as portions and quartiles. The validity test revealed high correlation for total flavonols, kaempferol, myricetin and isorhamnetin and moderate for quercetin. In the reproducibility analysis, the correlation was high for total flavonols, quercetin, kaempferol and myricetin, moderate for isorhamnetin and high for all 12 categories and 25 out of 27 subcategories of the tested food groups. The application of the FFQ in healthy adults and CAD patients revealed that dietary intakes of total flavonols and proportional intakes of kaempferol and isorhamnetin in Polish adults and CAD patients are higher than in most other European countries, while the proportional intakes of quercetin and myricetin are lower than in most European countries. The comparison between CAD patients and the healthy controls revealed significant differences in dietary isorhamnetin intake (p = 0.002). The results suggest that dietary isorhamnetin could have a potential role in CAD prevention.