ObjectivesUsing Geographical Information System (GIS) as a tool to determine access to and gaps in providing HIV counselling and testing (VCT), treatment (ART) and mother-to-child transmission (PMTCT) services in conflict affected northern Uganda.MethodsCross-sectional data on availability and utilization, and geo-coordinates of health facilities providing VCT, PMTCT, and ART were collected in order to determine access. ArcView software produced maps showing locations of facilities and Internally Displaced Population(IDP) camps.FindingsThere were 167 health facilities located inside and outside 132 IDP camps with VCT, PMTCT and ART services provided in 32 (19.2%), 15 (9%) and 10 (6%) facilities respectively. There was uneven availability and utilization of services and resources among districts, camps and health facilities. Inadequate staff and stock-out of essential commodities were found in lower health facility levels. Provision of VCT was 100% of the HSSP II target at health centres IV and hospitals but 28% at HC III. For PMTCT and ART, only 42.9% and 20% of the respective targets were reached at the health centres IV.ConclusionAccess to VCT, PMTCT and ART services was geographically limited due to inadequacy and heterogeneous dispersion of these services among districts and camps. GIS mapping can be effective in identifying service delivery gaps and presenting complex data into simplistic results hence can be recommended in need assessments in conflict settings.