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Femoral head necrosis (FHN) is a skeletal problem in broiler chickens, where the proximal femoral head cartilage shows susceptibility to separation from its growth plate. The selected birds with FHN showed higher body weights and reduced plasma cholesterol. The proteomic differences in the plasma of healthy and FHN-affected chickens were explored using matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS) and liquid chromatography/electrospray ionization-tandem mass spectrometry (LC-MS/MS) to prospect for protein biomarkers. We isolated two differentially expressed low molecular weight proteins and identified them by MALDI peptide mass fingerprinting as fibrinogen- and fetuin-derived peptides, respectively. These peptides were reduced in birds susceptible to femoral head problems. Quantitation of LC-MS/MS spectra showed elevated levels of gallinacin-9, apolipoprotein A1, and hemoglobin and reduced levels of alpha-1-acid glycoprotein, albumin, and SPINK7 proteins in FHN. These results suggest that the bodyweight and the lipid profiles along with the above proteins can be useful as noninvasive biomarkers of FHN.