We investigate the effect of the crustal structure heterogeneity and uncertainty in its determination on stripped gravity field. The analysis is based on interpretation of residual upper mantle gravity anomalies which are calculated by subtracting (stripping) the gravitational effect of the crust (including topography) from the observed satellite gravity field data (GOCE Direct release 3). We apply our analysis to Siberia for which a new regional crustal model has recently become available. Uncertainties in the residual upper (lithospheric) mantle gravity anomalies result from several sources: (i) uncertainties in the velocity-density conversion and (ii) uncertainties in knowledge of the crustal structure (thickness and average Vp velocities of individual crustal layers, including the sedimentary cover). In this study, we address both sources of possible uncertainties by applying different conversions from velocity to density and by introducing variations into the crustal structure which corresponds to the uncertainty of its resolution by high-quality and low-quality seismic models. We examine the propagation of these uncertainties into determinations of lithospheric mantle density. The residual mantle gravity anomalies are mainly caused by a heterogeneous density distribution in the uppermost mantle. Additionally, separation of the temperature effects from the residual upper mantle gravity anomalies provides constraints of the density changes due to variations in mantle composition. Given a relatively small range of expected density variations in the lithospheric mantle, knowledge on the uncertainties associated with incomplete knowledge of density structure of the crust is of utmost importance for further progress in such studies