Objective: Many factors including obesity were reported as risk factors for development and progression of chronic kidney disease (CKD). However, there is a possibility that the effects of risk factors on the progression of renal dysfunction in CKD patients and the development of CKD are different. We aimed to evaluate the relationships of visceral fat area (VFA) and changes in kidney function in medical checkup participants stratified by the presence of CKD for investigation of the effect of visceral fat on CKD development and progression. Design and method: Study design: Retrospective cohort study. Setting: Routine medical checkups at two medical examination centers in Takeda Hospital Group. Participants: Subjects who underwent VFA measurements during medical checkups in 2012. The follow-up period was from April 2012 to March 2018. Exposures: VFA (≧ 100 cm2). Main outcomes: Changes in estimated glomerular filtration rate (eGFRcr). Statistical analysis: The relationships between VFA and eGFRcr were evaluated using a linear mixed effects model in the participants stratified by the presence of CKD. We defined CKD as eGFR < 60 mL/min/1.73 m2 in this study. Results: Analysis was performed on total 2,753 subjects (age [mean ± SD] 50.3 ± 10.0 years). The non-CKD group was composed of 2,516 subjects (age 49.5 ± 9.67 years, 1,277 men, 1,239 women), and the CKD group was composed of 237 subjects (age 59.5 ± 8.48 years, 142 men, 95 women). In the total subjects the VFA ? 100 cm2 group exhibited a larger annual difference in eGFRcr compared to the < 100 cm2 group (-0.24 mL/min/1.73 m2, p = 0.03). Although the difference of annual eGFRcr change in the non-CKD group was not statistically significant, VFA? 100 cm2 was associated with larger annual declines in eGFRcr in both CKD and non-CKD groups as compared to VFA < 100 cm2 (-0.64 mL/min/1.73 m2, p = 0.01, and -0.20 mL/min/1.73 m2, p = 0.10). Conclusions: In the CKD group VFA ≧ 100 cm2 was significantly associated with a greater annual decline in eGFRcr. This significant difference of eGFRcr decline in the CKD group suggests the effect of visceral fat as a modifiable risk factor for CKD progression.