In this paper, we have combined molecular dynamics simulation and neutron diffraction experiments with polarization analysis, to unravel the different atomic correlations contributing to the total and partial static structure factors of polyisoprene (PI), Four different PI samples have been investigated: PId3 (methyl group deuterated and main chain protonated); PId5 (methyl group protonated and main chain deuterated); PId8 (fully deuterated); PIh8 (fully protonated), The neutron diffraction experiments with polarization analysis were carried out by means of the diffuse scattering spectrometer D7 at the Institute Lane Langevin (ILL, Grenoble, France). By means of this technique tile partial static structure factors corresponding to the PIh8, PId3, and PId5 samples and the total static structure factor S(Q) (PId8) were obtained in absolute units in the wavenumber regime Q less than or equal to 4 Angstrom (1). In addition, the temperature evolution of S(Q) was also measured by a neutron powder diffractometer (D20, ILL) without polarization analysis but in a wider Q range Q less than or equal to 13 Angstrom(-1). On the other hand, fully atomistic molecular dynamic (MD) simulations were carried out at different temperatures on a model of PI built by means of the amorphous-cell protocole. The static structure factors measured on the different samples were also calculated from the simulation data. The agreement found between simulation and measurements shows that our simulation cell is a realistic representation of the actual structure of PI. Taking advantage of the information contained in the simulation runs, we have unambiguously identified the different atomic correlations contributing to the different "peaks" of the total and partial structure factors measured. In particular, we have shown that a "prepeak" present in some of the data is not related to intermediate range order but is naturally explained by the interplay of the different partial structure factors, a result which may have some bearing also for other systems. In addition, we have found-both by experimental and by simulations-that the intensity of the first intermolecular peak of the total static structure factor S(Q) strongly increases with temperature. Although a full understanding of this phenomenon will need further work, we have been able to identify the main atomic correlations involved in this temperature evolution.