A number of physiological changes follow prolonged skeletal muscle unloading as occurs in space flight, bed rest, hind-limb suspension (HLS) and also in ageing. These include muscle atrophy, fibre-type switching, and loss of the ability to switch between lipid and glucose usage, also known as metabolic inflexibility. The signalling and genomic events that precede these physiological manifestations have not been investigated in detail, particularly in regard to loss of metabolic flexibility. Here we used gene arrays to determine the effects of 24h HLS on metabolic remodelling in mouse muscle. Acute unloading resulted in differential expression of a number of transcripts in soleus and gastrocnemius muscle, including many involved in lipid and glucose metabolism. These include the peroxisome proliferator activated receptors (PPARs). In contrast to Ppar- and Ppar- which were down-regulated by acute HLS, Ppar- was up-regulated concomitant with increased expression of its downstream target, uncoupling protein-3 (Ucp-3). However, differential expression of Ppar- was both acute and transient in nature, suggesting that regulation of PPAR may represent an adaptive, compensatory response aimed at regulating fuel utilisation and maintaining metabolic flexibility.