To assess the association between very short daily non-exercise physical activity (PA) lasting <5 min and metabolic syndrome (MS). A total of 42 females (50 ± 6 years) wore a pedometer with a one-axial accelerometer (Lifecorder, Kenz, Japan) to determine the time and the frequency of PA and the moderate to vigorous intensity PA (MVPA). In addition to the PA and the MVPA (PA(all) and MVPA(all)), the PA and MVPA were analyzed based on the bout duration, such as >32 s, >1 min, >3 min, and >5 min (PA(32S), PA(1M), PA(3M), PA(5M); MVPA(32S), MVPA(1M), MVPA(3M), MVPA(5M)). MS was defined according to the Japanese standard based on waist circumfluence, blood lipids, blood glucose, and blood pressure. The frequency of the MVPA(1M) was significantly lower in subjects with MS compared with that in subjects without MS (P < 0.05). The frequency of MVPA(32S) and MVPA(1M) was significantly associated with the HDL cholesterol (P < 0.05). The frequency of PA(3M) and PA(5M) was significantly associated with the fasting glucose level (P < 0.05). In contrast, we could not find any significant relationships between MS and the components of MS and the frequency of PA lasting <32 s. These results demonstrated that very short non-exercise PA, such as MVPA lasting >32 s to 3 min, has significantly associated with the components of MS. The specific advantages with regard to PA lasting <32 s remain unclear.