Background: Amputation and pain may have considerable impact on health-related quality of life. Objectives: The purpose of this study was to assess the impact of pain on health-related quality of life in a population of war related bilateral lower limb amputees. Materials and Methods: The Veterans and Martyrs Affairs Foundation (VMAF) database documented 578 patients with bilateral lower limb amputation; 335 consented to the study (response rate = 58%). The majority of participants in the sample were males (96.7%). Types of pain were investigated using a questionnaire. Health-related quality of life (HRQOL) was investigated using the sf-36 questionnaire. Results: About two third of amputees reported phantom pain 66.7% (n = 223) and vertebral column pain 60.9% (n = 204). The most common type of pain was lumbosacral pain 52.8 % (n = 177) followed by neck 18.2 % (n = 61) and thoracic pain 9.6% (n = 32). Back pain affected on vitality, social function, mental health and mental component scale in our cases (P < 0.05). Neck pain affected all components of health-related quality of life (P < 0.05). Thoracic pain affected quality of life significantly (P < 0.05). The results obtained from logistic regression analysis indicated that none of the three spinal column pains including neck, thoracic and lumbosacral pain resulted in poor physical or mental component scales. Conclusions: This study revealed that bilateral lower limb amputees suffer from different types of pain and poor health-related quality of life. Therefore, the assessment and management of all types of pain are necessary to improve quality of life in veterans.