PurposeTo demonstrate that interleaved MR thermometry can monitor temperature in water and fat with adequate temporal resolution. This is relevant for high intensity focused uUltrasounds (HIFU) treatment of bone lesions, which are often found near aqueous tissues, as muscle, or embedded in adipose tissues, as subcutaneous fat and bone marrow.MethodsProton resonance frequency shift (PRFS)‐based thermometry scans and T1‐based 2D variable flip angle (2D‐VFA) thermometry scans were acquired alternatingly over time. Temperature in water was monitored using PRFS thermometry, and in fat by 2D‐VFA thermometry with slice profile effect correction. The feasibility of interleaved water/fat temperature monitoring was studied ex vivo in porcine bone during MR‐HIFU sonication. Precision and stability of measurements in vivo were evaluated in a healthy volunteer under non‐heating conditions.ResultsThe method allowed observing temperature change over time in muscle and fat, including bone marrow, during MR‐HIFU sonication, with a temporal resolution of 6.1 s. In vivo, the apparent temperature change was stable on the time scale of the experiment: In 7 min the systematic drift was <0.042°C/min in muscle (PRFS after drift correction) and <0.096°C/min in bone marrow (2D‐VFA). The SD of the temperature change averaged over time was 0.98°C (PRFS) and 2.7°C (2D‐VFA).ConclusionsInterleaved MR thermometry allows temperature measurements in water and fat with a temporal resolution high enough for monitoring HIFU ablation. Specifically, combined fat and water thermometry provides uninterrupted information on temperature changes in tissue close to the bone cortex.