The present paper is aimed at assessing the economic efficiency of organically farming agricultural enterprises in a chosen region of the Czech Republic. The results recorded in the organic farming sector were confronted both with conventional agriculture and FADN (Farm Accountancy Data Network) enterprises in the respective region. Economic efficiency has been evaluated firstly by means of a production base (equity, assets, and liabilities). Secondly, profit indicators (operating profit, accounting profit) have been employed while monitoring the share of profitable and loss-making farms. Different profitability ratios were calculated per one hectare of farmland in order to provide a thorough comparison with conventional farming. Last but not least, the research strived to assess the overall economic and financial situation of agricultural enterprises by means of the following ratios: profitability, liquidity, indebtedness, interest coverage and total assets turnover. Following the research findings, several suggestions related to the database improvement and subsequent profitability assessment in the sector were formulated. The findings presented in the paper were obtained as a result of the Research Program titled Economy of the Czech Agriculture Resources and Their Efficient Use within the Framework of the Multifunctional Agri-food Systems of the Czech Ministry of Education, Youth and Sports number VZ MSM 6046070906 and Grant No. 20121057 of the Internal Grant Agency titled Organic Farming – Map Portal Presentation Opportunities.