The aim of this study was to analyze the association between chronic low back pain (LBP) in chronic post-traumatic stress disorder (PTSD) with quality and intensity of pain experience. 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). On the basis of medical records, interviews and different types of self-assessment questionnaires the inter-relationship between chronic pain and chronic PTSD was analyzed. PTSD was assessed by TSI-A (Trauma symptom Inventory, whereas pain was measured by Melzack-McGill Pain Questionnaire - short form (MPQ-SF) and Visual Analogue Scale (VAS). The patients with chronic PTSD had significantly higher total pain scores as well as affective and sensory pain components when compared to the patients without PTSD. No significant association was found between chronic LBP and symptoms of PTSD. Chronic LBP as functional painful syndrome in PTSD could be result of altered neuroanatomical and neurophysiological pain pathway and one of the markers of PTSD.