Introduction Measurement of the NMR frequency of water protons is one of the most sensitive ways to measure magnetic fields. Small susceptibility differences within tissue placed in a strong magnetic field give rise to effects which are well measurable by NMR and visualised in MR phase images. The information contained in the phase contrast between different tissue types is being increasingly used, for example to enhance visualisation of the vasculature in magnitude images [1], or to visualise subcortical structures with higher CNR than in magnitude images [2]. However, the microscopic origin of the susceptibility contrast between tissue types is not fully understood. Differences between distributions of capillaries, iron content, exchange with, and content of, macromolecules, and myelin content, have been proposed as contributors to the phase contrast between white and grey matter in the brain [2-4]. The quantitative interpretation of phase contrast is further complicated by geometrical effects and the fact that a well localised variation in susceptibility can give rise to much more extended variations in the magnetic field [5]. With the aim of contributing to the clarification of the origin of phase contrast, we investigated a post mortem rat brain with high-resolution (60μm isotropic) MRI. The phase contrast after formalin fixation was characterised in the whole brain and compared with T2* maps and cellular structure based on histology. Methods MR imaging was performed on a home-built 7T animal scanner based on Siemens software and hardware and a 210mm bore superconducting magnet (Magnex) equipped with a gradient coil with maximum gradient strength of 400mT/m/axis and 170μs rise time. RF excitation and reception was performed with a surface coil of 3cm diameter. The brain of a male Wistar rat was investigated after storage in 6% formaldehide solution for 14 months. For the MRI examination, the brain was placed in a plastic container of 2cm diameter and 3cm height filled with Fomblin (perfluoro-polyether, Solvay Solexis). The parameters of the dual echo 3D gradient echo sequence used for imaging included: TR=80ms, TE=4.5ms and 14.5ms, alpha=50 deg, 2 averages, FOV=31mm x 25mm, matrix=512x416, slice thickness 60μm, 192 slices. Twenty separate scans were acquired over a period of 2 days and the complex data were averaged off-line using Matlab. After averaging, the phase images corresponding to each echo were unwrapped using PRELUDE (FSL) and the field map was calculated from a linear fit to the phase as a function of TE. The smooth contribution to the field variation was obtained by applying a Gaussian filter with FWHM of 24x20 pixels to the Fourier transform of the field map, slice-byslice, and taking the inverse Fourier transform of the resulting matrix. The field maps discussed in the following were obtained by subtracting the smooth field variation from the original field map.