The Yale Animal Resource Cost and Benchmarking survey, conducted in United States (US) academic animal research/resource centres (ARC), was modified to capture similar information in European Union (EU) (including the non-EU countries Switzerland and the United Kingdom) academic ARCs, who are members of the League of European Research Universities (LERU). Participating institutions came from Denmark, England, Finland, France, Germany, Ireland, Italy, Netherlands, Scotland, Spain and Switzerland. Survey data analysis suggests that (a) per diem rates have similar compositions in LERU and US programs, with >50% of the rates dedicated to recovering salary and fringe, followed by supplies (∼25%), facility costs (∼10%) and other expenses (∼15%); (b) ∼60% of US and LERU programs under-recover mouse care costs; (c) on average, LERU programs have a small positive net-operating balance, while US programs average a large deficit; (d) in LERU programs <50% of institutions fund the animal program deficit, while in US programs almost 100% of such deficits are covered by the institution; and (e) when setting per diem rates, both US and LERU programs rank cost accounting as the most influential factor. Both US and LERU programs are reluctant to raise per diem rates to the extent required to recover costs and, thus, continue to under-recover costs, resulting in the animal program being ‘caught in the middle’ between the competing financial challenges of investigator ‘affordability’ and the animal program’s fiduciary responsibility to the institution.