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The objective was to estimate HIV-1 prevalence among women attending an antenatal clinic in the Gulu District (North Uganda) and based on these data among the districts female population. Anonymous HIV-1 screening was performed for 8555 antenatal clinic attendees aged 15-39 years in the period 1993-97. The results were used to estimate the prevalence among the districts female population accounting for differences in fertility rates by HIV-1 serostatus. Among antenatal clinic attendees HIV-1 prevalence showed a significant linear decrease (P < 0.001) from 26.0% in 1993 [95% confidence interval (CI) 23.2-29.0%] to 16.1% in 1997 (95% CI 14.8-17.5%). This decrease was mostly due to a marked decrease until 1995 (14.3%; 95% CI 12.7-16.0%) and was more pronounced among women aged under 30 years (P < 0.001) from both urban and rural areas (P < 0.001). The risk of being infected was higher among women from urban areas (Gulu Municipality) both over the entire period (adjusted prevalence proportion ratio = 1.54; 95% CI 1.40-1.68) and by individual year. The estimated prevalence for the 15-39 year old female population standardized by age and area of residence decreased from 25.4% in 1993-94 to 17.8% in 1996-97; these rates were 1.22 and 1.28 times higher respectively than those among antenatal clinic attendees. The trend of decrease among young women for whom changes in HIV-1 prevalence more closely reflect incidence could be partially due to a reduction in risk behavior and a consequent decreasing incidence. Differences in fertility rates by HIV-1 serostatus should be addressed when using antenatal clinic data to estimate prevalence among the general female population. (authors)