The primary objective of the study was to evaluate the correlation between prostaglandin F2-alpha and tumour necrosis factor-alpha concentration and that of pain experienced by patients undergoing thermal balloon ablation. Furthermore we evaluated the correlation between the endometrial and myometrial thicknesses and the degree of pain experienced by patients undergoing the procedure, and in addition the correlation between PGF2-alpha, TNF-alpha and endometrial and myometrial thicknesses. Single-arm cohort study (Canadian Task force classification II-2). In University Medical Centre Ljubljana, outpatient setting, 40 perimenopausal women with dysfunctional uterine bleeding (DUB), underwent endometrial thermal balloon ablation. The thickness of the endometrium and myometrium was measured prior to surgery using a transvaginal ultrasound that provided cross-sectional images. The degree of pain was rated using the visual analogue scale (VAS) and numeric rating scale (NRS) immediately and 60 minutes after the procedure. The concentration of PGF2-alpha and TNF-alpha in venous blood was measured prior to, at the end of and 60 minutes after the procedure. The results showed a positive correlation between the concentration of PGF2-alpha released during endometrial ablation and the endometrial and myometrial thickness (p > 0.01), including the reported degree of pain (p > 0.01). The concentration of TNF-alpha indicates a positive correlation with the level of pain (p > 0.05), but is not dependent on the thicknesses of the endometrium and myometrium. Endometrial thickness correlates to the degree of pain and the prostaglandin F2-alpha concentration. In clinical practice, performing the Gynecare ThermaChoice procedure immediately after menstruation or preoperative preparation of the endometrium using oral contraceptives enables this procedure to be performed in outpatient settings and can be considered a valuable treatment option for DUB.