Muscle atrophy and deconditioning are the major causes of poor functional status of patients following injuries or surgical procedures on musculoskeletal structures. Ischemia-reperfusion injury, caused by sustained ischemia during surgery, greatly influences the development of atrophy. Short termed periods of ischemia intermittent by reperfusion, so called ischemic conditioning, have been shown to attenuate the ischemia-reperfusion injury. The aim of this article is to systematically review scientific evidence of skeletal muscle protection induced by various protocols of ischemic conditioning and present potential protocols of its application before or after upper and lower limb surgery. Reviewed research presents evidence of increased cell viability, decreased cell injury and preservation of energy stores in preconditioned subjects. Despite the abundant evidence on acute protective effects, long-term effects of IP on development of muscle atrophy have not yet been investigated. There is clearly a need for determination of optimal IP protocol for clinical practice. Accurate measurements of cross-sectional area or muscle volume with magnetic resonance imaging, standardized muscle strength and function tests performed in crucial time intervals following surgery are the next logical step in the research of long-term effects of IP on human skeletal muscle.