Farmers participating in agri-environmental schemes (AESs) that are aimed at protecting biodiversity should ideally make decisions relating to the ecological management of their farms based on the habitat types found on their farms. In reality, a variety of economic, demographic, farm and farmer characteristics influence all the management decisions made by farmers, including those relating to AESs. In Ireland, the Rural Environment Protection Scheme (REPS) requires that farmers choose at least 2 biodiversity undertakings (BUs) from a menu as part of their AES contract. Using a multinomial logit model, the likelihood of farmers choosing different BUs was estimated using data from the 2007 National Farm Survey as a function of georeferenced habitat data. A comparison was then made between the probable selection of BUs with what would be considered the optimal selection from an ecological perspective. The results indicate that farmers' most likely choices of BUs only sometimes equates with the optimal ecological choices. This highlights deficiencies in the design of REPS, knowledge of which is very timely, given the imminent replacement of REPS by a new AES. (C) 2011 Elsevier B.V. All rights reserved.