Quantitative magnetisation transfer (MT) analysis is based on a two-pool model of magnetisation transfer and allows important physical properties of the two proton pools to be assessed. A good signal-to-noise ratio (SNR) for the measured signal is essential in order to estimate reliably the parameters from a small number of samples, thus prompting the use of a sequence with high SNR, such as a three-dimensional spoiled gradient acquisition. Here, we show how full brain coverage can be accomplished efficiently, using a three-dimensional acquisition, in a clinically acceptable time, and without the use of large numbers of slice-selective radio-frequency pulses which could otherwise confound analysis. This acquisition was first compared in post mortem human brain tissue to established two-dimensional acquisition protocols with differing SNR levels and then used to collect data from six healthy subjects. Image data were fitted using the two pool model and showed negligible residual deviations. Quantitative results were assessed in several brain locations. Results were consistent with previous single-slice data, and parametric maps were of good quality. Further investigations are needed to interpret the regional variation of quantitative MT quantities.