The effect of transport stress on superoxide production and adenosine phosphate concentration in addition to avian uncoupling protein (avUCP), avian adenine nucleotide translocator, and avian peroxisome proliferator-activated receptor-gamma coactivator-1alpha mRNA levels of skeletal muscles in broilers was investigated. Arbor Acres chicks (n = 360, 46 d old, males) were randomly allotted to 1 of 5 treatments: unstressed control, 45-min (short-term) transport with 45-min (short-term) recovery, 45-min transport with 3-h (long-term) recovery, 3-h (long-term) transport with 45-min recovery, and 3-h transport with 3-h recovery. Each treatment consisted of 6 replicates with 12 birds each. All birds (except control group) were transported according to a designed protocol. Transport time affected reactive oxygen species production in the thigh muscle (P < 0.05), adenosine triphosphate (ATP) content and energy charge (EC) in both breast and thigh muscles (P < 0.05 for all 4 comparisons), ATP:adenosine diphosphate (ADP) ratio in the breast muscle (P < 0.05), and avUCP mRNA levels in the thigh muscle (P < 0.05). Long-term transport increased (P < 0.05) reactive oxygen species production, ATP content, ATP:ADP ratio, and EC in the thigh muscle, but it decreased ATP content, ATP:ADP ratio, and EC in the breast muscle. Long-term transport increased avUCP mRNA in the thigh muscle (P < 0.05). Long-term recovery increased the ATP (P < 0.05) and ADP (P < 0.05) concentrations, avian adenine nucleotide translocator mRNA (P < 0.05), and avian peroxisome proliferator-activated receptor-gamma coactivator-1alpha mRNA (P < 0.05) in the thigh muscle, whereas EC decreased (P < 0.05) in the breast muscle. There were interactions between transport and recovery time on ATP (P < 0.05), EC (P < 0.05), and avUCP mRNA level (P < 0.05) in the thigh muscle. This study suggests that long-term transport accelerates muscle energy metabolism and lipid peroxidation. A long-term recovery may help alleviate cellular damage and maintain meat quality by reducing the rate of energy metabolism and scavenging of free radicals formed.