Purpose: Fatty acid (FA) abnormalities have been found in various inflammatory disorders and have been related to disturbed gut microbiota. Patients with Common variable immunodeficiency (CVID) have inflammatory complications associated with altered gut microbial composition. We hypothesized that there is an altered FA profile in CVID patients, related to gut microbial dysbiosis. Methods: Plasma FAs were measured in 39 CVID patients and 30 healthy controls. Gut microbial profile, a food frequency questionnaire and the effect of the oral antibiotic rifaximin, were investigated in CVID patients. Results: The n-3 PUFAs, EPA (1.4 [1.0-1.8] vs 1.9 [1.2-2.5], median [IQR], P<0.05) and DHA (3.2 [2.4-3.9] vs 3.5 [2.9- 4.3], P<0.05) were reduced in CVID compared to controls. Also, n-6 PUFAs (34.3 ± 3.4, vs 37.1 ± 2.8, mean ± SD, P< 0.001) and linoleic acid (LA) (24.5 ± 3.3, vs 28.1 ± 2.7, P< 0.0001), and the FA anti-inflammatory index (98.9, [82.1-119.4], vs 117.0, [88.7-153.1], median [IQR]), P<0.05) were reduced in CVID. The microbial alpha diversity was positively associated with plasma n-6 PUFAs, (r=0.41, P<0.001) and LA (r=0.51, P<0.001), but not n-3 PUFAs (P= 0.78). Moreover, a 2-week course of rifaximin significantly reduced the proportion of n-6 PUFAs (P=0.04, UNIANOVA). Overall, the altered proportions of n-3 and n-6 PUFAs did not seem to be related to dietary intake, intestinal malabsorption or presence of CVID enteropathy.Conclusion: We found a potentially unfavourable FA profile in CVID, where plasma proportion of n-6 PUFAs was related to gut microbial diversity and altered by microbial therapy.