Data are limited on the sex-specific prevalence of diseases and their risk factors in middle-aged and older workers in Japan. In this cross-sectional study, we investigated the age- and sex-specific prevalence of hypertension, diabetes, dyslipidemia, metabolic syndrome (defined using joint statement criteria), obesity, underweight, abdominal obesity, and smoking among approximately 70,000 to 90,000 Japanese workers (predominantly men) aged 20-69 years in 2014. We also investigated the prevalence of low cardiorespiratory fitness in 2012 and no leisure-time exercise in 2014. In both sexes, the prevalence of lifestyle-related risk factors, including hypertension, diabetes, dyslipidemia, metabolic syndrome, obesity, and abdominal obesity, was increased with aging. In contrast, the prevalence of underweight was decreased with aging. Smoking prevalence exceeded 30% in men regardless of age, whereas the prevalence was around 10% in women of all age groups. Prevalence of no leisure-time exercise exceeded 50% among middle-aged and older workers in both sexes. Among workers aged 50-64 years, less than half of men had low fitness, whereas more than half of women had low fitness. Given the high prevalence of lifestyle-related risk factors among middle-aged and older workers, effective strategies to prevent cardiovascular disease in this age group are needed in Japan.