The pathological mechanisms underlying peroxisomal biogenesis disorders (PBD) are not fully understood and the available therapies are not sufficient. This stresses the importance of identifying biochemical markers that reflect the extent of peroxisomal dysfunction in plasma of PBD patients.Very long chain fatty acids VLCFAs, Phytanic acid, inflammatory markers: tumor necrosis-alpha, interleukin-6, and interleukin-2 (TNF-alpha, IL-6, and IL-2), lipid peroxidation parameter malonedialdhyde (MDA), low density lipoprotein-cholesterol (LDL-C), high density lipoprotein-cholesterol (HDL-C), and catalase activity were measured.Significant increases in LDL-C, VLCFAs (C26:0, C26:0/C22:0 and C24:0/C22:0), Phytanic acid, MDA, and Catalase were observed along with significant decreases in Plasmalogen and HDL-C level. No significant difference could be found between male and female patients regarding the biochemical parameters. Both cholesterol and triglycerides showed no significant difference between patients and controls. The characteristic curve (ROC) showed that VLCFAs were the most significant diagnostic markers for PBD followed by TNF-alpha, IL2, IL6, MDA, and plasmalogens.PBD patients have impaired anti-oxidative defense together with increased inflammatory markers. We provide biomarkers that could guide therapies and prevention strategies. Based on our results we suggest clinical trials to investigate the role of dietary supplementation of antioxidants such as vitamin C and E as an adjuvant therapy for PBD patients.