The proton resonance frequency (PRF) shift provides a means of measuring temperature changes during minimally invasive thermotherapy. However, conventional PRF thermometry relies on the subtraction of baseline images, which makes it sensitive to tissue motion and frequency drift during the course of treatment. In this study, a new method is presented that eliminates these problems by estimating the background phase from each acquired image phase. In this referenceless method, a polynomial is fit to the background phase outside the heated region in a weighted least-squares fit. Extrapolation of the polynomial to the heated region serves as the background phase estimate, which is then subtracted from the actual phase. The referenceless method is demonstrated on a phantom during laser heating, 0° temperature rise images of in vivo human liver, interstitial laser ablation of porcine liver, and transurethral ultrasound ablation of canine prostate. A good correlation between temperature maps reconstructed with the referenceless and subtraction methods was found. Magn Reson Med 51:1223–1231, 2004. © 2004 Wiley-Liss, Inc.