Study Design: Basic science animal research study. Objectives: Using T10 spinal contused rats, we sought to identify molecular and circulating, metabolic and immune biomarkers during the subchronic and chronic recovery periods that may inform us concerning neurorehabilitation. Methods: Gene expression of the cord and ELISA were performed in 28 and 100 days in T10 injured rats and compared to sham-injured rats. Hundred-day injured rats were placed on either a low-fat or high-fat diet following the recovery phase. Linear regression analysis was performed between markers and locomotor score, body weight, body composition, and blood cholesterol and triglycerides. Results: Gene expression in the thoracic cord for complement marker, C1QC, dendritic cell marker, ITGAX, and cholesterol biosynthesis genes, FDFT1, HMCGR, LDLR, and SREBP1, were significantly associated with BBB score, body weight, composition, and other metabolic parameters. Circulating levels of these proteins, however, did not vary by injury or predict the level of locomotor recovery. Conclusions: Identification of reliable circulating biomarkers that are durable and based on level of spinal injury are complicated by immune and metabolic comorbidities. Continued work is necessary to identify stable markers of disease progression.