The aim of this study was to assess the associations of the body mass index (BMI), waist circumference (WC), and waist-to-height ratio (WHtR) with ischemic heart disease (IHD) and risk factors of IHD in the Lithuanian population aged 25 to 70 years. The cross-sectional health survey was carried out in Kaunas, which is the second largest city in Lithuania, and in five regions randomly selected from the northern, southern, eastern, western and central parts of Lithuania. Data from 2048 subjects (936 men and 1112 women) were analyzed. In both sexes, the odds ratios for reduced high density lipoprotein cholesterol, elevated triglycerides, high fasting blood glucose, and hypertension rose with an increasing quartile of BMI, WC, and WHtR. The likelihood of having IHD was statistically significantly higher in the fourth quartile of these anthropometric measures when compared to the first one. Comparison of the logistic regression models revealed that the models with WHtR best fit the prediction of IHD risk. Compared with BMI and WC, WHtR showed a stronger association with IHD and its risk factors in the Lithuanian adult population.