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Cytokines are important players in the homeostasis of the immune system in those infected with HIV. A study of 50 newly-infected HIV patients and 50 controls was completed with a 12-month follow-up. Before the start of therapy pro-inflammatory cytokines: Tumor necrosis factor-alpha (TNF-a), Interleukin-6 (IL-6), and anti-inflammatory cytokines: Interleukins 4 and 10 (IL-4 and IL-10) as well as Transforming growth factor beta (TGF-b) were elevated. After the start of therapy and compared to controls TNF-a and TGF-b remained elevated at 12 months but IL-4, IL-6 and IL-10 showed no significant differences from the control subjects at 12 months. Interferon gamma was reduced at both baseline and follow-up. While treatment does appear to reduce IL’s 4, 6, and 10 to levels of controls, the effect on other cytokines will take a longer follow-up period to understand the balance in the immune system and the apparent continuation of pro-inflammatory cytokines.