Introduction: In addition to enhanced protein catabolism, the cancer patient has alterations in lipid metabolism. Objective: The objective of the study was to evaluate serum concentrations of fatty acids (FA) before, during and after cancer treatment of patients with gastric or esophageal cancer. Subjects: The prospective longitudinal study was conducted with 14 patients with gastric or esophageal cancer [62.1 years (95% CI 55.6 to 68.6)], under cancer treatment in a specialized unit. The study also included 15 healthy volunteers [61.0 years (95% CI 57.1 to 65.0)]. Methods: The food intake questionnaires were applied (24-hour Dietary Recall) and inquiries related adverse effects and toxicity (CTCAE) that potentially interfere with food intake and nutritional status. Anthropometric measurements were made, the bioelectrical impedance and blood collection for laboratory tests. Gas chromatography determined the FA that was expressed as a percentage of the total area. In Cancer Group, the procedures were done before the start, the middle and at the end of cancer treatment; the control group underwent the same evaluations on only one occasion. Statistical analysis was performed using Statistica 8.0 software, using non-parametric statistical tests. Results: Adverse reactions related to cancer treatment have been reduced food intake, thick saliva with altered taste and nausea. Before the treatment, the patients with cancer had already lost 17% of weight with respect to the usual. Body weight and BMI reduced between the first and the third evaluation, but there was no change in the composition of lean and fat mass, energy intake and macronutrient most during the study. Compared to the control group, the nervonic acid was higher while the gamma-linolenic and alpha-linolenic acids were lower in the cancer group. In the longitudinal evaluation, the lignoceric acid reduced during cancer treatment. Conclusion: Patients with esophageal and stomach cancer have a mild change in the concentration of serum FA compared to controls and cancer treatment had little impact on the current FA profile.