BackgroundHepatitis B virus (HBV) exerts an intense impact on host lipid metabolism. Hence the aim of present study is to determine metabolic derangement that occurred in subjects suffering from hepatitis B patients.MethodsThe fasting blood samples were collected from hepatitis B patients (n = 50) attended in Taluka hospital TandoAdam, Sindh with age and gender matched controls (n = 50). Serum lipid profile and fatty acid (FA) composition were analyzed by micro-lab and gas chromatography.ResultsThe hepatitis B patients have significantly lower level (p < 0.01) of lipid profile including total cholesterol (TC), triacylglyceride (TAG), high density lipoprotein-C (HDL-C) very low density lipoprotein-cholesterol (VLDL-C), low density lipoprotein-cholesterol (LDL-C), and total lipid (TL) in comparison to controls, indicating hypolipidemia in patients. The result of total FA composition of HBV patients in comparison to controls reveal that myristic, palmitic, docosahexaenoic acids were significantly (p < 0.05) higher, while linoleic, eicosatrienoic, arachidonic, eicosapentaenoic acids were lower in HBV patients in comparison to controls. The elongase, ∆5 and ∆6-desaturase enzymes activities were found lower, while ∆9-desaturase activity was higher in hepatitis B patients as compared to controls, which indicates the impaired lipid metabolism.ConclusionThe serum saturated fatty acid (SFA) and monounsaturated fatty acid (MUFA) were increased while polyunsaturated fatty acid (PUFA) was reduced in both total and free form in hepatitis B patients due to altered activities of enzyme desaturases with impaired PUFA metabolism and non-enzymatic oxidation.Electronic supplementary materialThe online version of this article (10.1186/s12944-018-0683-y) contains supplementary material, which is available to authorized users.