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There are pointed out the problems in geological modeling of oil and gas deposits, arising during synthesis of particular stratum digital models into a single integrated model. It is shown, that only a system approach to the initial information, including concept development for stratum formation history and deposit accumulation, brings a possibility to build a whole deposit model consistent with geological principles. It is also shown, that the differentiated approach to various modeling objects allows one to build a 3D geologic model adequate to the initial data, which provide increase in reserve estimation reliability. There are given examples, when the integrated object structure revision has allowed the creation of non-contradictive geologic model.