Complying with the European Union (EU) perspective on human rights goes or should go together with handling ethical, social and legal challenges arising due to the use of biometrics technology as border control technology. While there is no doubt that the biometrics technology at European borders is a valuable element of border control systems, these technologies lead to issues of fundamental rights and personal privacy, among others. This paper discusses various ethical, social and legal challenges arising due to the use of biometrics technology in border control. First, a set of specific challenges and values affected were identified and then, generic considerations related to mitigation of these issues within a framework is provided. The framework is expected to meet the emergent need for supplying interoperability among multiple information systems used for border control.