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BACKGROUND: The international nongovernmental organization "AVSI Foundation" has been actively supporting Ugandas Ministry of Health (MoH) prevention of mother-to-child HIV transmission (PMTCT) program since 2002 in 4 districts of the conflict-ridden Acholi subregion in Northern Uganda. OBJECTIVE: This article presents data covering 10 years of MoH/AVSI PMTCT program activities in Northern Uganda. METHODS: The program followed Uganda MoH PMTCT guidelines and aimed to be comprehensive emphasizing social and medical care and support. Data were collected from 24 health facilities from January 2002 to December 2011. Trend analyses were carried out using Predictive Analytics SoftWare (PASW) Statistics 18. RESULTS: Of the 140658 women who newly attended antenatal care services from 2002 to 2011 94.4% received HIV testing and counseling and 6.2% tested HIV-positive. HIV testing and counseling of male partners of tested pregnant women steadily increased from 5.9% in 2002 to 75.8% in 2011 compared with 15.5% in 2011 nationally. Overall 79.0% of HIV-positive women were started on antiretroviral prophylaxis (69.4%) or triple antiretroviral therapy (9.6%) compared with 52% nationally in 2011. The proportion of HIV-positive women who delivered in health facilities significantly increased from 55.8% in 2004 to 81.1% in 2011 (no national data available). HIV prevalence among HIV-exposed infants tested at or below 18 months of age significantly decreased from 10.3% in 2004 to 5.0% in 2011. CONCLUSIONS: Our results show how a comprehensive PMTCT program emphasizing social and community engagement alongside medical care and support can succeed in a remote setting with multiple challenges.