The aim of this study was to analyze the association between single nucleotide polymorphism (SNP) in IL1B (rs1143 634) and IL1RN (rs2234677) with chronic low back pain (LBP) in chronic post-traumatic stress disorder (PTSD). A total of 406 war veterans from 1991-1995 war in Croatia participated in this study. They were divided into four groups, according to psychiatric interview, psychometric testing and the presence of LBP, verified by the imaging of lumbar area, into: (i) war veterans suffering from PTSD and LBP (N = 102), (ii) war veterans suffering from PTSD only (N = 108), (iii) war veterans suffering from LBP only (N = 99) and (iv) healthy controls (N =97). Each subject provided a blood sample for IL1B and IL1RN polymorphism testing. We found no association of rs1143634 in IL1-B with LBP Permutation test showed significant association of rs1143634 in IL1-RN with LBP group and presence of wild type allele A was protective in LBP group. The same SNP (rs1143634) in IL1-B was associated with the intensity of pain. No other associations were observed between these two markers and self-reported measures evaluating PTSD and pain symptoms. These results suggest the potential role of cytokine network in the pathogenesis of chronic PTSD and LBP, although the direct causative pathway remains unclear. The alteration of cytokine network on the level of the brain, spinal medulla and the spine may be responsible for modulation of pain and the occurrence of LBP