We address the problem of completely characterizing multi-particle states including loss of information to unobserved degrees of freedom. In systems where non-classical interference plays a role, such as linear-optics quantum gates, such information can degrade interference in two ways, by decoherence and by distinguishing the particles. Distinguishing information, often the limiting factor for quantum optical devices, is not correctly described by previous state-reconstruction techniques, which account only for decoherence. We extend these techniques and find that a single modified density matrix can completely describe partially-coherent, partially-distinguishable states. We use this observation to experimentally characterize two-photon polarization states in single-mode optical fiber.PACS numbers: 03.65. Wj,05.30.Jp,42.50.St The development of techniques for characterizing pure and mixed quantum states has enabled many advances in quantum information and related fields. Whether in order to study the effects of decoherence [1], to optimize the performance of quantum logic gates [2], to quantify the amount of information obtainable by various parties in quantum communications protocols [3], or to adapt quantum error correction protocols to real-world situations [4], it is first necessary to obtain as complete a characterization as possible of the state of a given quantum system (or ensemble). In the general case of mixed states, this involves reconstruction of a density matrix, a mathematically complete description of the degrees of freedom of interest in a quantum system. Entanglement with experimentally inaccessible or 'hidden' degrees of freedom (sometimes called "the environment") enters the density matrix as a reduction in the off-diagonal coherences. In some quantum systems -those composed of multiple particles that cannot be individually addressed -reduced coherence can only partially describe the effects of hidden degrees of freedom. Another phenomenon, distinguishability, arises when hidden degrees of freedom provide information that could in principle be used to tell the particles apart without necessarily leading to any changes in the coherences of the density matrix. This paper will show how a density matrix characterization of such states can be performed while taking into account the decoherence and distinguishability as distinct phenomena.Systems of particles that cannot be individually addressed occur commonly in quantum optics and elsewhere. A central example is the Hong-Ou-Mandel (HOM) effect [5], in which non-classical interference causes photon bunching at a beamsplitter. The effect results in photons with the same characteristics entering the same mode, making it impossible to individually address the photons, i.e., to manipulate or measure them individually. Many other major results in the field of quantum optics such as the generation of Bell states, the demonstration of teleportation [6], linear optics quantum computing [7], the generation of cluster states [8] and the demonstration o...