Background Maintaining a good level of physical fitness from engaging in regular exercise is important for the treatment and prevention of metabolic syndrome (MetS). However, which components constitutive of physical fitness confer the greatest influence remains controversial. This retrospective cross-sectional study aimed to investigate the association between MetS and physical fitness components including cardiorespiratory fitness, muscle strength, flexibility, and agility and to identify which physical fitness components have the largest influence on MetS. Methods A total of 168 Japanese adult males aged 25–64 years were allocated into non-MetS, pre-MetS, and MetS groups according to the criteria recommended by the Japanese Society of Internal Medicine. Anthropometric measurement of body composition by whole-body dual-energy X-ray absorptiometry and measures related to MetS, including waist circumference, triglyceride level, high-density lipoprotein cholesterol level, blood pressure, glucose level, and physical fitness components, were assessed. For evaluation of cardiorespiratory fitness, muscle strength, flexibility, agility, and balance, maximal oxygen consumption (VO2peak) and oxygen uptake at anaerobic threshold (VO2AnT), handgrip strength and vertical jumping, trunk extension and flexion, stepping side to side, and single-leg balance task with the eyes closed were assessed, respectively. Results A progressive tendency of increasing body weight, body mass index, whole-body lean and fat mass, percentage of whole-body fat mass, trunk lean and fat mass, percentage of trunk fat mass, arm fat mass, waist circumference, triglyceride level, systolic and diastolic blood pressure, and blood glucose level from the non-MetS group to the MetS group was significant (P < 0.05). Conversely, the cardiorespiratory endurance parameters VO2peak and VO2AnT and the high-density lipoprotein cholesterol level showed a progressively decreasing tendency across the groups (P < 0.01). In addition, a VO2peak below 29.84 ml·kg·min−1 (P = 0.028) and VO2AnT below 15.89 ml·kg·min−1 (P = 0.011) were significant risk components for pre-MetS and MetS. However, there was no significant tendency with respect to muscle strength, agility, and flexibility. Conclusion Cardiorespiratory fitness is strongly linked to metabolic syndrome among physical fitness components
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