For the first time it was conducted complex research of metabolic disorders in patients co-infected with HIV/HCV and was shown that they are characterized by disturbances of mineral, lipid and carbohydrate metabolism types. It was established significantly higher values of indicators of mineral, lipid and carbohydrate metabolism types in patients co-infected with HIV/HCV compared with patients with chronic hepatitis C and HIV-infected persons. In patients co-infected HIV/HCV appears significantly more frequent the polymorphism Asp299Gly of the gene TLR4 (χ2 = 4,5; p<0,05) when compared with healthy donors, which plays a significant role in the development of metabolic disorders, such correlation is confirmed by those relationships: a strong direct relationship between the polymorphism Asp299Gly of TLR4 gene and the content of insulin (r = 0,66; p<0,001), insulin resistance (r=0,66; p<0,001), the absolute number of CD45+ of T-lymphocytes (r=0 45; p<0,001); a moderate direct relationship with the content of TNF-α (r=0,32; p<0,05), CRP (r=0,34; p<0,05), the absolute number of CD3+ of T-lymphocytes (r=0,34; p<0,05), the content of triglyceride (r=0,39; p<0,02), moderate inverse relationship with the zinc content (r = -0,34; p<0,05 ), the relative number of CD4 +,% (r = -0,32; p<0,05). The system of monitoring of metabolic disorders in patients co-infected with HIV/HCV based on the definition of polymorphism Asp299Gly gene TLR4, the presence of which indicates a high risk of metabolic disturbances (OR=23,3; p<0,05) and requires further investigation, namely the definition of an index of insulin resistance, insulin levels, TNF-α, C-reactive protein, zinc and triglyceride levels in dynamics at intervals of 6 months that allow for timely diagnosis and correction of metabolic disorders.