Background: Although Eastern Europe, including Estonia, has one of the highest morbidity and mortality rates associated with hypertension, there is little information in the literature concerning the biochemical risk factor profile or its association with hypertension in Estonia. This study examined the cross-sectional gender-stratified association between biochemical risk markers and hypertension in a population-based sample of adults in Estonia. Methods: The study was carried out in Tallinn, Estonia and consisted of 511 men and 600 women with a mean age of 46 years. Physiological measurements were taken and blood samples drawn to measure the following markers: cholesterol, high- and low-density lipoprotein cholesterol, apolipoproteins A-1 and B, lipoprotein(a), triglycerides, glucose, fibrinogen, high-sensitivity C-reactive protein and homocysteine. Results: Overall, 36% of participants had hypertension, with approximately 80% being aware of their condition. A total of 40% of participants reported taking antihypertensive medication. Multivariate binary logistic regression analysis showed that a decrease in high-density lipoprotein cholesterol and increases in age, body mass index, apolipoprotein B, triglyceride and homocysteine levels were associated with an increased probability of hypertension. Conclusions: Elevations in biochemical markers and cardiovascular risk factors are associated with hypertension. Increasing body mass index, triglyceride, apolipoprotein B and homocysteine levels with decreasing high-density lipoprotein cholesterol level should be investigated and monitored in Estonian adults.