The availability of new food choices has increased dramatically in recent times, whilst increasingly sedentary lifestyles have reduced calorie intake requirements. The present study uses 24 hour dietary recall data, and biochemical and anthropometric measurements from the 1993-1996 and 2005-2008 Nutrition and Health Surveys in Taiwan (NAHSIT) to investigate trends in dietary habits, and cardiovascular and metabolic disease markers in Taiwanese persons aged 19 years and above. We found that dietary habits in Taiwan are changing, particularly in regards to intakes of cakes and sweets, and sugary drinks. Energy intakes in young people have increased, and combined with an increasingly sedentary lifestyle, this may have led to the increase in obesity and associated metabolic diseases. Large increases in the prevalence of the metabolic syndrome, diabetes, hypertriglyceridemia and gout have been observed. Fortunately, some positive dietary and behavioral changes have also been observed; including an increased avoidance of products made from animal fats and oils' and a concomitant increase in the use of vegetable oil. Intakes of fruit and vegetables, soy products, fish, whole grains, nuts and seeds have also increased; and intakes of red meat, carbohydrates and sodium containing foods have decreased. These positive dietary changes could explain the lack of large changes in the prevalence of hypertension and hypercholesterolemia, and the decrease in prevalence of hyperuricemia. Intake of dairy products remains low, and continues to be an important dietary issue in Taiwan.