(R)-9-(2-phosphonylmethoxypropyl)adenine (PMPA), an acyclic phosphonomethyl ether nucleoside analogue, acts as a reverse transcriptase inhibitor and has shown potent in vivo efficacy against acute SIV infection in adult and newborn macaques. The current study evaluated the effects of PMPA treatment in chronically SIV infected macaques. For this study, nine cynomolgus macaques (Macaca fascicularis) that had been chronically infected with SIV mne for at least 19 weeks were treated with PMPA (30 mg/kg); or with PMPA (75 mg/kg). The agent was administered subcutaneously in a single daily dose for four weeks. The clinical and virologic status of the macaques was evaluated weekly throughout treatment and periodically thereafter. The efficacy was evaluated by monitoring cell-free and cell-associated virus load, cell-associated viral DNA, plasma viral RNA levels and absolute numbers of lymphocyte subsets. Although SIV was undetectable by PBMC coculture from animals treated with PMPA, the animals continued to have SIV DNA as determined by PCR. In conclusion, PMPA showed significant inhibition of SIV during treatment, however, SIV reappeared after treatment was stopped.