OBJECTIVE: The objective of this study was to compare the nutrient content of foods and diets based on data from two food composition databases used in the Baltic Nutrition Surveys (conducted in Estonia, Latvia and Lithuania in 1997): an adapted version of the Finnish Micro-Nutrica Nutritional Analysis program (used in Estonia) and the Russian Institute of Nutrition Food Composition Database (used in Latvia and Lithuania). DESIGN: The adapted Micro-Nutrica and Russian databases were used to estimate the energy and nutrient (protein, fat, carbohydrate, vitamin C, calcium and iron) content of 15 common foodstuffs in the region and the nutrient intakes of 32 Latvian respondents (based on 24-h recalls). Differences between databases were estimated. RESULTS: There were discrepancies in the energy and nutrient content of the 15 selected foods using the two databases. The adapted Micro-Nutrica database generally gave a lower energy content than the Russian database (median: -6%), and a lower fat content for typically fat-rich foods. Intakes of energy, fat, carbohydrate and calcium by the 32 selected respondents were significantly lower when the Micro-Nutrica database was used. Differences were particularly high for fat (difference=-23.5%, 95% confidence interval=-31.1 to -15.8%, P<0.0001). CONCLUSIONS: The results suggest that reported comparisons of nutrient intakes in the Baltic countries should be treated with caution and that more research is needed for the development of comparable national databases in the region. Potential differences between databases should be investigated early when international surveys of dietary intake are being planned.