Côte d'Ivoire is one of the most affected countries in West Africa with HIV/AIDS, with a prevalence of 3.4%. Essential amino acids are needed by the organism as they play key roles in the immune system and they are supplied through diet. The objective of this study was to determine the plasma lysine and threonine status for better medical and nutritional management of patients living with HIV. This study involved 254 individuals: 127 HIV positive and 127 HIV negative (serving as controls) after confirmation of their HIV status through an HIV test (test DETERMINE® and GENIE II). Lysine and threonine were assayed using high performance liquid chromatography (HPLC) on plasma and CD4 lymphocyte count by the method of flow cytometry (FacsCalibur) from whole blood containing EDTA. This study showed that deficiency of lysine was more observed in male HIV infected individuals (66.7%) and threonine deficiency in female HIV infected individuals (17.1%) as compared to the controls subject. The amino acid concentrations as a measure of the degree of immunosuppression was significant for lysine (P = 0.0006) and not significant for threonine (P = 0.8640). The deficiency observed in HIV infected patients taking antiretrovirals is therefore probably due to viral infection and insufficient lysine intake in diet. The threonine concentration depends on the health condition of the subject.