Improvements in physical wellbeing during the first six months on antiretroviral therapy (ART) are well known, but little is known regarding more long-term follow-up. We conducted a prospective cohort study among 222 HIV-positive adult tea plantation workers in western Kenya to assess wellbeing over their first two years on ART. Study subjects completed a standardized questionnaire during repeat ART clinic visits. A 30-day recall period was used to elicit the number of days that subjects experienced poor health and the number of days that pain made it difficult to complete usual activities at home and work. A seven-day recall period was used to assess the severity of bodily pain, nausea, fatigue and rash. Prevalence of most symptoms declined over time. A median of 7 days poor health during the first month on ART declined to 3 days in the 24^th month (p=0.043). For pain making usual activities difficult, a median of 7 days during the first month on ART fell to 0 by 12 months (p≤0.0001) but increased to 3 days by two years. Any bodily pain (range 59-83%) and fatigue (range 51-84%) over the past 7 days were common through 2 years. However, pain and fatigue often over the past 7 days declined over two years (24% to 10% (p=0.067) and 41% to 15% (p=0.002)). Skin rash was rare at all times, though higher at two years (8.6%) than any other time. Initial improvements in physical wellbeing were sustained over two years, however, increased pain and skin rash at year two, may indicate problems as treatment programs mature. These improvements in physical wellbeing will be important in sustaining the long-term success of HIV treatment programs.