Reported high immunization coverage achieved in Nepal over the last ten years is expected to reduce child mortality in the country. The present study, carried out in hill district in mid-west Nepal, aimed to assess the quality of immunization data in Nepal. The number of children who received different vaccines during one year was obtained from three sources: 1) the Immunization REgister of three Primary Health Care Service Outlets (PHCSOs) where each immunized child is recorded; 2) monthly PHC Reports, which are based on the Immunization Register; 3) monthly DHO Reports, which are based on the above PHC Reports (the DHO reports are the source of official statistics). The number of children in the PHC Reports was higher than the number in the Immunization REgisters for all vaccines. The number of immunizations in the DHO Reports was higher than the number in the PHC Reports for BCG, DPT, and measles; the number was lower for poliomyelitis. The overall number of immunizations was higher in the DHO Reports than in the Immunization Registers, by 31% for BCG, 44% for DPT, 155% for polio, and 71% for measles. We conclude that the official report overestimates the immunization coverage in the district. The immunization programme, therefore, might not result in the expected reduction of morbidity and mortality despite the investment in the programme and reported high coverage.