Summary Background & aims Arachidonic (AA) and eicosapentaenoic (EPA) polyunsaturated fatty acids can play respectively a pro- and an anti-inflammatory role. We hypothesized that, at the end of 5-week experimental bed rest, baseline AA/EPA in red blood cells (RBC) membranes, considered the result of dietary fat intake over the previous month, could influence lean body mass wasting in twenty-six healthy volunteers (age: 23.5 ± 0.5 years; body mass index: 22.9 ± 0.5 kg/m2). Methods We measured AA and EPA content in RBC membranes at baseline ambulatory conditions and at the end of the study protocol, to verify the PUFA concentrations stability. We assessed changes, between beginning and end of bed, in lean body mass (bioimpedance), insulin resistance (homeostasis model assessment), systemic inflammation (C-reactive protein) and oxidative stress (thiobarbituric acid reactive substances). Volunteers were divided in two groups according to the AA/EPA ratio median value (i.e. AA/EPA = 44): High AA/EPA group (60 ± 3; n = 13) and Low AA/EPA group (37 ± 1; n = 13). Results At baseline, all analyzed anthropometrical and biochemical indices were similar in the two groups. Bed rest induced a major decrease in lean body mass in High AA/EPA group (−5.2 ± 0.5%), when compared to Low AA/EPA group (−3.7 ± 0.5%; p = 0.03; ANOVA). Bed rest mediated-changes of insulin resistance, fat mass, systemic inflammation and oxidative stress, failed to show significant interaction with baseline AA/EPA (ANOVA). In pooled data, baseline AA/EPA ratio and percent lean body mass delta changes showed a significant inverse correlation (n = 26; R = −0.50; p Conclusions Results suggest that baseline AA/EPA, in RBC membranes, can independently predict lean body mass wasting in immobilized subjects during long term disuse.