Background The existence of social withdrawal (Hikikomori), which meets the conditions “not attending school”, “not working”, and “isolated at home for more than 6 months”, is gradually being discovered by the world, and their mental health and healing is being highlighted. However, there are very few Hikikomori-related surveys searching their physical health, as it is generally believed that most Hikikomori are adolescents. Middle-aged Hikikomori are also found outside Japan, and their physical health is more important, because Hikikomori have difficulty managing their health due to the socially isolated circumstances and lack of sociability. Although “isolated at home for more than 6 months” could not be used, we extracted a group with low social independence with reference to Hikikomori-related surveys. We estimate that people with low social independence have similar characteristics and problems to Hikikomori, because they share many causes for the problem of difficulty in managing their own health. People with low social independence were identified, and their physical health, such as smoking and drinking status, consultation rates of various diseases, and how often they attend cancer screenings, was analyzed. Methods We extracted middle-aged people with low social independence and a control group from the national survey in Japan and stratified them by sex and age. Their health risks were assessed by univariate analysis. Criteria for the experimental group were set with reference to Hikikomori-related surveys. Criteria for the control group included “aged 40–69”, “living with parents”, “not receiving care for disabilities”, and ”working”. Results Low-social-independent men had higher consultation rates for diabetes, stroke or cerebral hemorrhage, myocardial infarction or angina, gastric and duodenum diseases, kidney disease, anemia, and depression, while lower consultation rates for dyslipidemia and hypertension. The tendency of non-smoking and non-drinking was found among them. They seldom attended cancer screenings. Low-social-independent women had higher consultation rates for liver and gallbladder diseases, other digestive diseases, kidney diseases, anemia, osteoporosis, and depression. The tendency of non-drinking was the same as men. More heavy smokers were found among those aged 40–49 years, with no significant differences in other age groups. They seldom attended cancer screenings, as well as men. Conclusions In terms of current physical health, low-social-independent men have more fatal diseases. Both sexes with low social independence seldom attend cancer screenings and have an increased risk of developing progressive cancer in the future. At least in terms of non-smoking and non-drinking, they live healthier lives than the control group, and what makes low-social-independent men have various fatal diseases is still unclear.