This study compared the antioxidant status and major lipophilic antioxidants in patients with ataxia-telangiectasia (AT) and Nijmegen breakage syndrome (NBS). Total antioxidant status (TAS), total oxidant status (TOS), oxidative stress index (OSI), and concentrations of coenzyme Q10 (CoQ10) and vitamins A and E were estimated in the plasma of 22 patients with AT, 12 children with NBS, and the healthy controls. In AT patients, TAS (median 261.7 μmol/L) was statistically lower but TOS (496.8 μmol/L) was significantly elevated in comparison with the healthy group (312.7 μmol/L and 311.2 μmol/L, resp.). Tocopherol (0.8 μg/mL) and CoQ10 (0.1 μg/mL) were reduced in AT patients versus control (1.4 μg/mL and 0.3 μg/mL, resp.). NBS patients also displayed statistically lower TAS levels (290.3 μmol/L), while TOS (404.8 μmol/L) was comparable to the controls. We found that in NBS patients retinol concentration (0.1 μg/mL) was highly elevated and CoQ10 (0.1 μg/mL) was significantly lower in comparison with those in the healthy group. Our study confirms disturbances in redox homeostasis in AT and NBS patients and indicates a need for diagnosing oxidative stress in those cases as a potential disease biomarker. Decreased CoQ10 concentration found in NBS and AT indicates a need for possible supplementation.