We have investigated the short-range order in 1,4-polybutadiene by combining fully atomistic MD simulations and neutron diffraction with polarization analysis on isotopically labeled samples. Thereby the structure factor corresponding to the fully deuterated sample and the partial structure factor of the fully protonated polymer have been obtained. Both functions show a first main peak centered at about 1.4 angstrom(-1) and a second one at around 3 angstrom(-1). With varying temperature, we observe opposite tendencies for the intensity of the first diffraction peak in each sample. The direct comparison between simulation and experimental data has allowed validation of our simulated cell. Exploiting the information on the simulations, we have found that CC correlations dominate the first diffraction peak for both the deuterated and the protonated samples, while the origin of the second maximum depends on the labeling. Finally, the temperature behavior of the first peaks has also been rationalized. To a large extent, density changes are driving the evolution of the peaks, and the way they affect mainly the CC correlations and the mixed correlations involving C and H determines the behavior observed in the diffraction patterns.