We describe and evaluate a method for intensity non-uniformity correction of whole-body fat-water MR data acquired with both surface and body coils on a 3T PET/MRI system. The proposed method consists of two steps. Abrupt station intensity changes are first supressed, followed by correction of smooth intensity changes using fat and water fraction information. Visual and quantitative evaluations of 42 corrected fat-water datasets show that the method gives improved adipose and lean tissue uniformity for both surface and body coil acquisitions. This renders the data suitable for continued analysis in a whole-body imaging framework.