BACKGROUND: It is uncertain whether the health counselling after community-based health checkups for high-risk individuals of lifestyle-related disease accelerates their referral to physicians. METHODS: We performed a clustered randomized controlled trial of untreated high-risk individuals aged 40 to 74 years, screened from the annual health checkup in 2014 and 2015 under the national health insurance in 43 municipalities around Japan, assigning 21 intervention and 22 usual care municipalities. The high-risk conditions were severe forms of hypertension, diabetes, dyslipidemia for men and proteinuria. For the intervention group, the theory-based health counselling was performed to accelerate referrals to physicians while its own counselling of each municipality for the usual care group. Data on clinical visits and risk factors were collected systematically and anonymously from the databases of health insurance qualification, health insurance claims and annual health checkups. Hypotheses are that the cumulative proportion of seeing physicians (clinical visits) is higher in the intervention than the usual care groups, and that those in the intervention group have the lower cumulative incidence of composite outcomes associated with lifestyle-related diseases. RESULTS: The number of subjects for the analyses were 8,977 in the intervention group and 6,733 in the usual care group. Among them, 6,758 had hypertension, 2,147 diabetes, 2,861 dyslipidemia, and 1,221 proteinuria in the intervention group, and 4,833, 1,517, 2,262 and 845 in the usual care group. There were no material differences in mean levels and proportions of major cardiovascular risk factors between the two groups. CONCLUSIONS: We expected to provide scientific evidence on the effectiveness of health counselling.