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The paper considers the results of calculation of the three-dimensional density model of the Earth’s crust for the territory of the Republic of Niger in conditions of incomplete initial geological and geophysical information. A brief description of the geological structure of the research region is given and the task of the study is formulated. The initial data set of density modeling is described, including: the anomalous gravity field, the initial model of the medium, the constraints on the desired solution, and the weight functions of redistribution of field incompatibilities. Inversion of the anomalous gravity field was performed in a three-dimensional formulation for a regular grid with a 25×25 km spacing in the plan and 14 layers of irregular vertical grid. The density model of the crystalline crust obtained by solving the inverse problem was combined with a priori data on the density of the upper mantle layer and the previously constructed layered model of the sedimentary cover of the region. The main features of the density model of the Earth’s crust are considered and its density heterogeneities are compared with the regional geological and tectonic data. The leading role of young structures of the West African rift System and their relationship with density inhomogeneities in the lower and middle crust of the territory of the Republic of Niger was noted.