Three groups of sedentary male rats were exposed to intermittent hypobaric hypoxia (IHH) for 22 days (4 h/day, 5 days/week) in a hypobaric chamber at a simulated altitude of 5,000 m. Tibialis anterior (TA) and diaphragm (DG) were removed at the end of the programme (H group), and 20 or 40 days later (P20 and P40 groups). A control group (C) was maintained at sea-level pressure and their TA and DG were compared to those of the experimental rats at the end of the IHH programme, and also 20 and 40 days later. We measured the fibre morphometry and capillaries of each muscle. Our results demonstrate that IHH does not change the fibre type composition (with reference to either their contractile or oxidative properties) for most muscle regions of the muscles analysed analysed. We found few significant differences in muscle capillarity and fibre morphometry for TA after IHH. However, IHH did induce some statistically significant changes in DG: capillary density of the H rats (736 capillaries/mm2) increased compared to C animals (610 capillaries/mm2). Although IHH did not change the fibre capillarization or morphometric parameters of fast fibre types, we observed reductions ranging from 7 to 13% in fibre area, perimeter and diffusion distances between C and H for slow fibres. Moreover, these morphometric changes accounted for increases of 10-20% in capillarization, fibre unit area and fibre unit perimeter. This indicates that SO fibres are more sensitive to IHH than both fast fibre types.