BackgroundA recent concept is that obesity, assessed by body mass index (BMI), is not always a sign of poor health. Thus, in order to use obesity metrics in clinical decision making, it is important to clarify the relationship between waist circumference (WC), a proxy for abdominal obesity, and mortality.MethodsData were used from 8,796,759 subjects aged between 30 and 90 years, who had participated in the Korea National Health Screening Examination between January 1, 2009 and December 31, 2009 and survived at least 1 year post screening. Data from a mean follow-up time of an additional 5.3 years (time at risk) were analyzed for the relationship between WC and mortality according to age, sex, and BMI category.ResultsAn increased WC of more than 90 cm in men and 85 cm in women showed a definite negative influence on mortality. However, the detailed relationship between WC and mortality was J-shaped or U-shaped according to age, sex, and BMI category. In the normal BMI group, the optimal WC range with the lowest mortality was < 70 cm in men and 70–75 cm in women, whereas in obese individuals a WC between 80 and 90 cm in men and 75 and 85 cm in women showed the lowest mortality. The association between increased WC and higher mortality tended to be more obvious in normal-weight women than in normal-weight men or obese women. Furthermore, in normal-weight and obese women, the effect of increased WC on mortality was more critical for subjects aged < 60 years rather than those aged ≥ 60 years.ConclusionsAbdominal obesity, as measured by WC, showed a significant negative association on mortality, and its association with mortality was different according to age, sex, and BMI category. Therefore, WC should be considered in the assessment of obesity-related health risks, and individualized cut-off points for the definition of a healthy WC according to age, sex, and BMI category are necessary.Electronic supplementary materialThe online version of this article (10.1186/s12916-018-1114-7) contains supplementary material, which is available to authorized users.