We estimated HIV incidence and identified risk factors for seroconversion following a rural community home based HIV counseling and testing program in Uganda. We analyzed data from two rounds of testing at least a year apart. Of 19,401 initially seronegative participants, 106 seroconverted in Round 2. Overall HIV incidence was 0.55 per 100 person years (95 % CI: 0.45 -0.66) with no gender difference. Among men, being widowed or divorced (aRR 4.4), and having HIV related symptoms (aRR 11.5) were associated with seroconversion; having primary level education (aRR 0.2) was protective. Among women, being aged 35-59 years (aRR 2.3) and having HIV related symptoms (aRR 9.2) were associated with seroconversion; having couples' posttest counseling in Round 1 (aRR 0.4) was protective. HIV incidence is lower than estimates from elsewhere in Uganda. Nevertheless, focused prevention programs are still needed, targeting previously married men and older women, and including couples' counseling.