Objective The patients affected by Crohn's disease (CD) present often with a malnutrition status, that may persists even after the acute phase of disease. The aim of this prospective study was to evaluate which effect may have surgical induced remission on the lipid and phospholipids profile. Method Thirty-seven patients, who underwent ileo-colonic resection for CD between December 2004 and April 2006, were enrolled in this prospective study. Anthropometric parameters, disease activity, diet, inflammatory parameters, lipid profile and serum phospholipids fatty acids (FA) composition were assessed at ileo-colonic resection and after 6 months. Data were expressed as mean (range) and t-test for paired data and Spearman correlations between percent variation (delta%) were used.Result The mean interval between resection and control was 6 (4-9) months. During this interval CRP serum levels decreased, even if not significantly, and albumin levels were significantly increased (38.0 vs 43.1g/l, p=0.015). In lipid profile the only modification was a significant increase of HDL cholesterol (from 48+/-19 to 57+/-19 mg/dl, p<0.01). Serum arachidonic acid (20:4 n6) and adrenic acid (22:4 n6) decreased significantly after 6 months of interval. A significant correlation between the delta% of weight and eicosanoic (20:1 n9) (r=-0.93, p= p<0.01) and eicosapentaenoic acid (EPA) (20:5 n3) (r=0.82, p=0.02) was observed. The delta% of CRP directly correlated with delta% of oleic acid (18:1 n9) (r=0.82, p=0.02) and with those of palmitoleic acid (16:1 n7) (r=0.82, p=0.02), and inversely with those of stearic acid (18:0) (r=-0.86, p=0.01). Conclusion The restoration of the intestinal physiological properties after ileo-colonic resection is probably the cause of HDL cholesterol increase since the HDL proteins are produced in the intestine. The serum fatty acid modifications, that were observed after the 6 months follow up, could be attributed to dietary modifications and to modification of the activities of the liver enzymes that regulates fatty acid metabolism (i.e. elongase and desaturase). In fact, the activity of these enzymes is strictly related to the disease activity.