We have previously reported that there may be a relationship between bowel habits including functional constipation (FC) and irritable bowel syndrome and sleep health. However, our previous studies were based on only subjective parameters by self-reported questionnaire. The aim of this study is to investigate the relationship between bowel habits such as FC and sleep health using objective parameters. Sleep health was assessed by actigraphy measurement and bowel habits by fecal flora analysis. The FC and control subjects, whose bowel habits were defined at Rome II, were recruited from evaluated respondents in our previous study directed at middle-aged Japanese women, ten FC and ten control subjects participating in this study. Wake after sleep onset (WASO) and WASO (%) (WASO/total sleep time multiplied by 100) in FC subjects was significantly longer and greater than those in control subjects, respectively. Average activity during sleep in FC subjects was significantly higher than that in control subjects. FC had no effect on total sleep time. Bifidobacterium is broadly accepted to be useful intestinal bacteria for human health and one of the indices showing that the intestinal environment is in a desirable condition. Bifidobacterium counts per gram of wet feces and proportion in total bacterial cell counts in FC subjects were significantly lower than those in control subjects. In conclusion, these results suggest that corresponding to low Bifidobacterium counts and proportion, sleep in FC subjects may be worse than that in control subjects. There may be a relationship between bowel habits and sleep health. Bowel habits such as FC might be a risk factor for sleep disorders.