The influence of microstructure of 9%Cr-1%Mo steel on the hydrogen diffusivity, solubility and hence the permeability was investigated using electrochemical permeation technique. This steel was austenitised and cooled at various cooling rates to produce different microstructures. Tempering behaviour was also studied by heat treating for different durations at 1023 K. Characterisation of microstructures was carried out using scanning electron microscopy and analytical transmission electron microscopy. A fully martensitic product was obtained during fast cooling and a mixture of proeutectoid ferrite and martensite during slow cooling. Tempering the normalised steel resulted in the formation of fine intragranular M2X precipitates and M23C6 on the boundaries. The hydrogen diffusivity and solubility showed a regular trend with the amount of strain in the lattice. Lattice defects and precipitates act as trap sites for hydrogen. Increase in lattice strain either due to increase in defect density, substructure or coherent precipitates resulted in decrease in diffusivity due to increase in trap sites. Martensite structure offered the maximum resistance to hydrogen diffusivity and tempered martensite the least resistance due to the annihilation of defects during tempering.