Early recognition of lameness is crucial for injury prevention. Quantitative gait analysis systems can detect low-grade asymmetries better than the human eye and may be useful in early lameness recognition. The aims of this study were (1) to investigate the frequency of gait asymmetries based on head and pelvic movement in elite eventing horses using inertial mounted measurement units and (2) to assess the association between asymmetries and muscle enzymes and blood lactate (LA) levelspost-exercise. Movement asymmetry of the head, wither, and pelvis were quantified in 33 elite eventing horses prior to and one day after the cross-country test of three Concours Complet International (CCI3* and CCI4*) events held three weeks apart. The effects of LA concentration immediately after completion of the cross-country course and of serum levels of creatine kinase (CK) and aspartate amino-transferase (AST) four hours post-exercise on gait asymmetry parameters were tested with linear models. A total of 58% and 77% of the 33 horses exhibited gait asymmetries that exceeded published threshold values before and after the cross-country course, respectively. The magnitude of pre-existing gait asymmetries was not significantly increased after the cross-country test and no associations with post-exercise levels of CK, AST, or LA were detected. The stride duration was significantly shorter the day following the cross-country test and was associated with LA, the age and the weight of the horses. In conclusion, a majority of the horses studied presented gait asymmetries and strenuous exercise resulted in decreased stride duration but did not worsen gait asymmetries.