Coeliac disease (CD) patients may exhibit a pro-inflammatory profile and fatty acids (FA) can influence inflammation through a variety of cellular pathways in them. The aims of the present study were to (1) evaluate the FA composition of erythrocytes obtained from newly diagnosed CD patients by lipidomic analysis and compare it with that in healthy subjects and (2) determine the effects of 1-year gluten-free diet (GFD) intervention. A total of twenty CD patients (five men and fifteen women; mean age 34.0 (sem 1.7) years) were evaluated at diagnosis and after 1 year of GFD intervention. A total of twenty healthy subjects (seven men and thirteen women; mean age 40.2 (sem 2.5) years) served as controls. CD patients on an unrestricted diet exhibited a significant 2.08-fold higher concentration of arachidic acid when compared with healthy subjects, suggesting that it can be considered as a putative marker of CD. Besides, the arachidonic acid (AA):dihomo-γ-linolenic acid ratio was 2.01-fold significantly lower in CD patients than in healthy subjects (P< 0.01), underlying an inefficient synthesis of PUFA from their precursors in terms of desaturase activity. In addition, mainly due to lower concentrations of docosahexaenoic acid, the inflammation marker AA:docosahexaenoic acid ratio was 1.40-fold significantly higher in CD patients than in healthy subjects. After 1 year of GFD intervention, FA concentrations in CD patients were still different from those observed in healthy subjects. The lipidomic analysis of erythrocyte membranes confirmed the presence of an altered FA composition in CD patients and the GFD's ability to modify FA profile, even if 1-year GFD intervention seems to be not sufficient to restore FA concentrations to normality. This procedure, being easier and non-invasive compared with the evaluation of the FA pattern of the intestinal mucosa, could offer more potentiality for also evaluating therapeutic interventions in CD patients by using FA supplementation.