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In this paper, we propose self-organizing schemes for the initial configuration of the neighbor cell list (NCL), maintenance of the NCL, and physical cell identifier (PCI) allocation in heterogeneous networks such as long term evolution systems where lower transmission power nodes are additionally deployed in macrocell networks. Accurate NCL maintenance is required for efficient PCI allocation and for avoiding handover delay and redundantly in creased system overhead. Proposed self-organizing schemes for the initial NCL configuration and PCI allocation are based on evolved universal terrestrial radio access network NodeB (eNB) scanning that measures reference signal to interference and noise ratio and reference symbol received power, respectively, transmitted from adjacent eNBs. On the other hand, the maintenance of the NCL is managed by adding or removing cells based on periodic user equipment measurements. We provide performance analysis of the proposed schemes under various scenarios in the respects of NCL detection probability, NCL false alarm rate, handover delay area ratio, PCI conflict ratio, etc.