Background Since 1986, North Uganda has been affected by civil strife and most of its population have been displaced in protected camps. However, since 2007, the increased security conditions have allowed many people to leave the camps and return to their villages. This study aims at estimating the HIV prevalence trend among pregnant women in Gulu district in the conflict (2005–2006) to post-conflict (2007–2010) transition period.

Methods In 2005–2006 and 2007–2010, a total of 2318 and 25,924 ANC attendees of the St. Mary’s Hospital Lacor, respectively, were anonymously tested for HIV within the national sentinel surveillance system. Differences in HIV prevalence by testing period and displacement status were evaluated using the chi-square test.

Results The overall HIV prevalence in 2005–2006 was 11.0% compared with 9.9% in 2007–2010 (P = 0.074). In both periods, as previously found, prevalence among internally displaced women (IDW) was lower than prevalence among women living outside camps. However, the difference in prevalence between these two groups decreased in the transition period. In fact, while the prevalence remained quite stable among IDW (9.2% in 2005–2006 compared with 8.3% in 2009–2010; P = 0.370), it significantly decreased among women living outside camps (12.6% in 2005–2006 compared with 10.4% in 2009–2010; P = 0.020), mostly reflecting the population movements occurred since 2007 (IDW were 45.0% of the ANC attendees in 2005–2006 compared with 27.5% in 2009–2010; P < 0.001).

Conclusions The HIV prevalence in Gulu district is still high compared with the rest of Uganda. It remained quite stable, thus suggesting that no HIV-related behavioural changes in the post-conflict period have occurred or that their effects are not yet observable. However, the reduced difference in HIV prevalence between IDW and women living outside of protected camps suggests that the HIV epidemiological profile in this district is changing, mainly as a result of the post-conflict population movements