The metabolome is the composition of all molecules present in an organism, metabolomics science allows us to qualitatively and quantitatively analyze metabolites and understand the biochemical state in response to genetic and environmental changes. The purpose of the study was to identify the metabolomic profile of biofluids (saliva and urine) of patients living with HIV/AIDS (PLHIV/AIDS), and establish a possible association of metabolites with periodontal disease (PD). It was an analytical and descriptive study composed of 65 patients seen at the Center for Studies and Care for Special Patients (CEAPE-UNIP), who were divided into 4 predetermined groups (G), G1-PLHIV/AIDS and without PD, G2- PLHIV/Aids and with PD, G3-people without HIV/Aids and without PD, G4-people without HIV/Aids and with PD. The results showed that in relation to urine, G2 has the highest mean area of concentration of metabolites. There are statistically significant differences between G1 and G2. The area of G2 is greater than G3, and greater than G4. There are no differences between G3 and G4, neither between G1 and G3, nor between G1 and G4. Regarding saliva, there are no statistically significant differences when comparing the groups for the mean areas of concentration of metabolites. We conclude that it was possible to distinguish the metabolic profile of PLHIV/Aids with periodontal disease and without periodontal disease, some metabolites are over expressed in PLHIV/Aids and with PD. Most of the metabolites of the carbohydrate group are under expressed in PLHIV/AIDS, even in systemic compensation situations these patients presented a different metabolic profile.