Abstract Aim This study used the measure of percentage of body fat (%BF) to define obesity and evaluated the effect of percentage of %BF on clinical, surgical and pathological features in women with endometrial cancer. Methods Between 2011 and 2013, bioelectrical impedance analysis and body size measurements of 94 patients whose endometrial biopsy revealed endometrial cancer were obtained. Patients were divided into two groups according to body mass index (BMI) (normal, <30 kg/m2; elevated, ≥30 kg/m2), and also classified by %BF (normal, <32%; elevated, ≥32%). Results The patients' mean age was 55.0 ± 10.9 years. Mean %BF and BMI were 40.8% ± 9.8% and 32.9 ± 7.5, respectively. Eighty-three (88%) patients were obese according to %BF; 54 (57%) were obese according to BMI. Patients with elevated %BF were more likely to have less than 50% myometrial invasion (P = 0.004). Significantly more para-aortic lymph nodes were retrieved in patients with normal %BF or BMI (P < 0.001, P < 0.001). Patients with elevated %BF had longer operating times (P = 0.043) and were more likely to have stage I disease than patients with normal %BF (P < 0.001). Conclusion Endometrial cancer patients with an elevated %BF are more likely to have stage I disease and less than 50% myometrial invasion than patients with normal %BF. Defining obesity by BF may provide better estimation of obesity prevalence in patients with endometrial cancer and further understanding the relationship between BF with endometrial cancer may give more information about the effects of obesity on endometrial cancer.