Background and Objectives: Glutamine is a nonessential amino acid which improves intestinal mucosal regeneration and absorption. Glutathione is a vital molecule for antioxidant reactions and is synthesized from cystine. The first aim of the study is to measure the plasma glutamine and cystine in children with celiac disease (CD) and compare them with controls. The second aim of this study is to investigate whether these amino acids are correlated with endomysial antibody (EMA) or not. Methods and Study Design: Fifty children with CD were compared to 50 healthy, age, and sex matched normal children as control. Plasma glutamine and cystine levels of the children were measured by using tandem mass spectrometry. Results: Plasma glutamine (808 vs 870 mu mol/L) and cystine (19 vs 48.5 mu mol/L) were significantly lower in the celiac group than the controls (p<0.05). The levels of plasma glutamine (797 vs 928 mu mol/L, n=42) and cystine (18 vs 31.5 mu mol/L, n=8) were lower (p<0.05) in the EMA-positive than the EMA-negative celiac patients. We could not find any statistically significance between EMA-negative celiac patients and controls for the plasma glutamine (928 vs 870 mu mol/L) and cystine (31.5 vs 48.5 mu mol/L) (p>0.05). Serum EMA was negatively correlated with plasma cystine (r=-0,321, p=0.023), glutamine (r=-0.413, p=0.003). Conclusions: Our study indicated that plasma glutamine and cystine were significantly lower in the celiac children than the controls. Also, these amino acids were negatively correlated with EMA.