BACKGROUND: This cross-sectional study sought to determine the neck-shoulder stiffness/low back pain (NSS/LBP) comorbidity rate in a Japanese community population and to compare the quality of life (QOL) in individuals with comorbid NSS/LBP, asymptomatic individuals, and those with symptoms of NSS or LBP alone. METHODS: The sample included 1122 subjects (426 men; 696 women) with NSS and LBP symptoms in the previous 3 months, and were grouped according to NSS, LBP, comorbid NSS and LBP symptoms (Comorbid), or no symptoms (NP). They completed the MOS 36-Item Short-Form Health Survey (SF-36). Health QOL was evaluated by the eight domain scores and the Physical Component Summary (PCS) and Mental Component Summary (MCS) scores after adjusting for age. The primary outcome was to examine the association between NSS/LBP, NSS, or LBP and bodily pain of the eight domains of SF-36. Secondary outcome was to compare health-related QOL among the four groups. RESULTS: Morbidity was 45.6% for NSS and 51.9% for LBP. Comorbidity affected 23% of men and 33% of women. Comorbid NSS/LBP, NSS, and LBP alone were independently associated with bodily pain after adjusting for potential confounders. Men who exhibited comorbidity had significantly lower MCS scores than asymptomatic men. Women who exhibited comorbidity and LBP had significantly lower MCS scores than those with no symptoms or NSS alone. Women who exhibited comorbidity had significantly lower MCS scores than those with no symptoms or LBP alone. CONCLUSIONS: Comorbidity of the two diseases is prevalent in 23% of the men and 33% of women in the Japanese sample. Although NSS, LBP, and comorbidity were independently associated with QOL in terms of pain, QOL was worse in individuals who exhibited comorbidity than in those without symptoms or with NSS alone.