Purpose To minimize the known biases introduced by fat in rapid T-1 and T-2 quantification in muscle using a single-run magnetic resonance fingerprinting (MRF) water-fat separation sequence.... Show morePurpose To minimize the known biases introduced by fat in rapid T-1 and T-2 quantification in muscle using a single-run magnetic resonance fingerprinting (MRF) water-fat separation sequence. Methods The single-run MRF acquisition uses an alternating in-phase/out-of-phase TE pattern to achieve water-fat separation based on a 2-point DIXON method. Conjugate phase reconstruction and fat deblurring were applied to correct for B-0 inhomogeneities and chemical shift blurring. Water and fat signals were matched to the on-resonance MRF dictionary. The method was first tested in a multicompartment phantom. To test whether the approach is capable of measuring small in vivo dynamic changes in relaxation times, experiments were run in 9 healthy volunteers; parameter values were compared with and without water-fat separation during muscle recovery after plantar flexion exercise. Results Phantom results show the robustness of the water-fat resolving MRF approach to undersampling. Parameter maps in volunteers show a significant (P < .01) increase in T-1 (105 +/- 94 ms) and decrease in T-2 (14 +/- 6 ms) when using water-fat-separated MRF, suggesting improved parameter quantification by reducing the well-known biases introduced by fat. Exercise results showed smooth T-1 and T-2 recovery curves. Conclusion Water-fat separation using conjugate phase reconstruction is possible within a single-run MRF scan. This technique can be used to rapidly map relaxation times in studies requiring dynamic scanning, in which the presence of fat is problematic. Show less