Although muscle and joint pains are among the most common symptoms in menopausal transition, their underlying mechanisms are not precisely known. This study aimed to investigate the factors associated with myalgia and arthralgia in middle-aged women. We analyzed in a cross-sectional manner the first-visit records of 305 Japanese women aged 40-59 years who enrolled in a health and nutrition education program at a menopause clinic. The prevalence of muscle and joint pains was estimated according to the participants' responses to the Menopausal Health-Related Quality of Life Questionnaire. Background characteristics including age, menopause status, body composition, cardiovascular parameters and physical fitness, as well as other menopausal symptoms including vasomotor symptoms, insomnia, depression and anxiety, were assessed for associations with daily myalgia and arthralgia. The percentage of women who were bothered by muscle and joint pains almost every day of the previous week was 56.1%. Characteristics associated with these symptoms were: low stature; high body fat percentage; low grip strength; and high vasomotor, insomnia, depression and anxiety symptom scores. Multivariate logistic regression analysis revealed that independently associated factors (adjusted odds ratio [95% confidence interval]) for daily myalgia/arthralgia were low hand-grip strength (kgf) (0.92 [0.87-0.97]) and insomnia symptom score (1.20 [1.07-1.34]). Muscle and joint pains are highly prevalent in Japanese middle-aged women. Low grip strength and insomnia are independently associated with these symptoms. Treatment of insomnia in this population might improve myalgia/arthralgia, and in turn, help restore grip strength, or treatment of hand pain might conversely reduce insomnia in addition to improvement in grip strength.