INTRODUCTION:: DOMS (Delayed-Onset Muscle Soreness), a condition triggered by eccentric exercise, affects muscle cells at a biochemical level in a poorly understood fashion. The objective of the present study was to examine human muscle proteome modifications induced by strenuous eccentric exercises following a specific training aimed to prevent DOMS. METHODS:: Biopsy of the rectus femoris were taken from healthy human volunteers in three successive conditions: (1) at rest, (2) 24 hours after an injuring exercise protocol consisting of 3 series of 30 maximal contractions of the quadriceps on an isokinetic dynamometer, (3) 24 hours after a similar exercise bout preceded either by 5 eccentric training sessions, or no training. RESULTS:: Muscle damage was assessed before and 1 day after each maximal eccentric test by comparing three indirect markers: plasma activity of creatine kinase (CK), muscle stiffness and subjective pain intensity. Compared to the first eccentric test, those markers were reduced after the second test and further reduced if this second test followed the eccentric training, thus confirming the protective effect of such training. Muscle protein extracts were subjected to a 2D-DIGE proteomic analysis coupled with MALDI-TOF-MS protein identification. Surprisingly, we observed that myosin heavy chains decreased after the first eccentric test, and were reduced further with other contractile proteins after the second test. Furthermore, the expression of several glycolytic enzymes decreased only after the second test that was preceded by a specific training. CONCLUSION:: These findings suggest that the eccentric training resulted in a switch to oxidative metabolism, which may be associated with protection from DOMS.