Introduction: Since the comprehensive peace agreement was signed in 2005, institutionalization of immunization services in South Sudan remained a priority. Routine administrative reporting systems were established and showed that national coverage rates for DTP-3 rose from 20% in 2002 to 80% in 2011. This survey was conducted as part of an overall review of progress in implementation of the first EPI Multi-Year Plan for South Sudan 2007-2011. This report provides maiden community coverage estimates for immunization.

Methods: A cross sectional community survey was conducted between January and May 2012. Ten cluster surveys were conducted to generate state-specific coverage estimates. The WHO 30x7 cluster sampling method was employed. Data was collected using pre-tested, interviewer guided, structured questionnaires through house to house visits.

Results: The fully immunized children were 7.3%. Coverage for specific antigens were; BCG (28.3%), DTP-1(25.9%), DTP-3 (22.0%), Measles (16.8%). The drop-out rate between the first and third doses of DTP was 21.3%. Immunization coverage estimates based on card and history were higher, at 45.7% for DTP-3, 45.8% for MCV and 32.2% for full immunization. Majority of immunizations (80.8%) were received at health facilities compared to community service points (19.2%). The major reason for missed immunizations was inadequate information (41.1%).

Conclusion: The proportion of card-verified, fully vaccinated among children aged 12-23 months is very low at 7.3%. Future efforts to improve vaccination quality and coverage should prioritize training of vaccinators and program communication to levels equivalent or higher than investments in EPI cold chain systems since 2007.