We conducted a cross-sectional survey of 12,988 subjects aged 20-79 years (5,908 men and 7,090 women) receiving health checkups at a Tokyo clinic. They filled out a self-administered structured questionnaire, and 5.4% of the men and 15.4% of the women reported having headaches. Younger subjects were more prone to having headaches. The likelihood of having headaches increased with stress level and decreased ability to relieve stress in both genders. There was an inverse dose-response relationship between having headaches and alcohol consumption, and less walking/exercise and sleep problems increased the likelihood of headaches in both genders. Headache sufferers of both genders were more likely to report multiple additional poor health conditions. A multivariate stepwise logistic analysis showed that age, self-estimated degree of stress, reported number of additional poor health conditions, and less alcohol consumption were independently correlated with having headaches. In conclusion, although women were more susceptible to headache, Japanese men and women in Tokyo shared factors associated with headache, including age, stress, having other poor health conditions, alcohol consumption, sleep, and exercise.