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Higher educational attainment has been associated with a greater risk of HIV infection in sub-Saharan Africa. We investigated change over time in HIV prevalence by educational attainment in the general population.The data stem from serial population-based HIV surveys conducted in selected urban and rural communities in 1995 (n = 2989), 1999 (n = 3506) and 2003 (n = 4442). Analyses were stratified by residence, sex and age-group. Logistic regression was used to estimate age-adjusted odds ratio of HIV between low (≤ 4 school years) and higher education (≥ 8 years) for the rural population and between low (≤ 7 school years) and higher education (≥ 11 years) for the urban population.There was a universal shift towards reduced risk of HIV infection in groups with higher than lower education in both sexes among urban young people [odds ratio (OR), 0.20; 95% confidence interval (CI), 0.05–0.73] in men and (OR, 0.33; 95% CI, 0.15–0.72) in women. A similar pattern was observed in rural young men (OR, 0.17; 95% CI, 0.05–0.59) but was less prominent and not statistically significant in rural women. In age 25–49 years, higher educated urban men had reduced risk in 2003 (OR, 0.43; 95%CI, 0.26–0.72) but this was less prominent in women.The findings suggested a shift in the association between educational attainment and HIV infection between 1995 and 2003. The most convincing sign was the risk reduction among more educated younger groups where most infections can be assumed to be recent. The changes in older groups are probably largely influenced by differential mortality rates. The stable risk among groups with lower education might also indicate limitations in past preventive efforts.