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Symmetry protected topological (SPT) phases are gapped phases of matter that cannot be deformed to a trivial phase without breaking the symmetry or closing the bulk gap. Here, we introduce a new notion of a topological obstruction that is not captured by bulk energy gap closings in periodic boundary conditions. More specifically, given a symmetric boundary termination we say two bulk Hamiltonians belong to distinct boundary obstructed topological phases (BOTPs) if they can be deformed to each other on a system with periodic boundaries, but cannot be deformed to each other in the open system without closing the gap at at least one high symmetry surface. BOTPs are not topological phases of matter in the standard sense since they are adiabatically deformable to each other on a torus but, similar to SPTs, they are associated with boundary signatures in open systems such as surface states or fractional corner charges. In contrast to SPTs, these boundary signatures are not anomalous and can be removed by symmetrically adding lower dimensional SPTs on the boundary, but they are stable as long as the spectral gap at high-symmetry edges/surfaces remains open. We show that the double-mirror quadrupole model of [Science, 357(6346), 2018] is a prototypical example of such phases, and present a detailed analysis of several aspects of boundary obstructions in this model. In addition, we introduce several three-dimensional models having boundary obstructions, which are characterized either by surface states or fractional corner charges. We also provide a general framework to study boundary obstructions in free-fermion systems in terms of Wannier band representations (WBR), an extension of the recently-developed band representation formalism to Wannier bands. WBRs capture the notion of topological obstructions in the Wannier bands which can then be used to study topological obstructions in the boundary spectrum by means of the correspondence between the Wannier and boundary spectra. This establishes a form of bulk-boundary correspondence for BOTPs by relating the bulk band representation to the boundary topology.