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We define a class of boundary value problems on manifolds with fibered boundary. This class is in a certain sense a deformation between the classical boundary value problems and the Atiyah-Patodi-Singer problems in subspaces (it contains both as special cases). The boundary conditions in this theory are taken as elements of the C*-algebra generated by pseudodifferential operators and families of pseudodifferential operators in the fibers. We prove the Fredholm. property for elliptic boundary value problems and compute a topological obstruction (similar to Atiyah-Bott obstruction) to the existence of elliptic boundary conditions for a given elliptic operator. Geometric operators with trivial and nontrivial obstruction are given. (c) 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim