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Background Lipedema is a painful subcutaneous adipose tissue (SAT) disorder that mainly affects women. Patients present fat accumulation in the limbs, especially in the legs. Methods A pilot-controlled clinical trial was conducted on a sample of 18 patients with lipedema, equally divided into a control group (CG) and an experimental group (EG). Both groups were given 10 sessions of diathermy on the inner side of their knees, 10 min of treatment per knee. EG was given the diathermy dose at high-intensity heat, while CG was given sham treatment. Measurement instruments used were circumferential measurements, ultrasound measurements, algometry, VAS, and SF-12 questionnaire. Data were collected at baseline, at the end of the study and 5 weeks later. Results significant reductions in left knee circumference were observed in the EG compared with the CG (p = 0.004 post-intervention and p = 0.017 at follow-up). No significant differences were found in ultrasound, algometry, or VAS measurements within or between groups. Conclusions High-intensity heat diathermy resulted in a reduction in knee circumference, suggesting a potential effect on limb volume.