The effect of hydrogen bonding to the primary quinone (Q_A and Q^˙−_A) in bacterial reaction centers was studied using density functional theory (DFT) calculations. The charge neutral state Q_A was investigated by optimizing the hydrogen atom positions of model systems extracted from 15 different X-ray structures. From this analysis, mean values of the H-bond lengths and directions were derived. It was found that the N_δ–H of His M219 forms a shorter H-bond to Q_A than the N–H of Ala M260. The H-bond of His M219 is linear and more twisted out of the quinone plane. The radical anion Q^˙−_A in the protein environment was investigated by using a mixed quantum mechanics/molecular mechanics (QM/MM) approach. Two geometry optimizations with a different number of flexible atoms were performed. H-bond lengths were obtained and spectroscopic parameters calculated, i.e. the hyperfine and nuclear quadrupole couplings of magnetic nuclei coupled to the radical. Good agreement was found with the results provided by EPR/ENDOR spectroscopy. This implies that the calculated lengths and directions of the H-bonds to Q^˙−_A are reliable values. From a comparison of the neutral and reduced state of Q_A it was concluded that the H-bond distances are shortened by ∼0.17 Å (His M219) and ∼0.13 Å (Ala M260) upon single reduction of the quinone. It is shown that the point-dipole approximation can not be used for an estimation of H-bond lengths from measured hyperfine couplings in a system with out-of-plane H-bonding. In contrast, the evaluation of the nuclear quadrupole couplings of ²H nuclei substituted in the hydrogen bonds yields H-bond lengths close to the values that were deduced from DFT geometry optimizations. The significance of hydrogen bonding to the quinone cofactors in biological systems is discussed.