Streptococcus pneumoniae (Sp.) is a leading cause of paediatric bacterial meningitis, pneumonia and acute otitis media, as is non-typable Haemophilus influenzae (NTHi) for acute otitis media. In 2008, a 7-valent conjugated pneumococcal vaccine (PCV7) was included in the New Zealand (NZ) childhood immunization schedule. To estimate the potentially vaccine-preventable annual hospital admissions and cost to the NZ Government of paediatric admissions for pneumococcal disease and NTHi otitis media prior to the immunization programme. Admissions (2000-7) and deaths (2000-5) in children aged<20 years with pneumococcal meningitis or bacteraemia, pneumonia or otitis media were identified in national datasets and linked by unique patient identifiers. New episodes of illness were defined as admissions occurring >30 days after discharge from a previous admission. Informed by the literature, pneumococcal pneumonia episodes were estimated at 33% of all-cause pneumonia admissions; Sp. and NTHi otitis media episodes were estimated jointly at 72% of otitis media admissions. Each episode was assigned a single diagnosis according to the following hierarchy: meningitis>bacteraemia>pneumonia>otitis media. Incidence rates for episodes were determined for 2000-7 (meningitis, bacteraemia and pneumonia) and 2006-7 (otitis media). Annual DRG-based costs for pneumococcal meningitis, bacteraemia, pneumonia and otitis media were estimated as (episode rate)x(DRG cost weight per episode)x(2007 population)x(national price per cost weight). Episode rates for pneumococcal meningitis, bacteraemia and pneumonia were stable in 2000-7, highest in the second 6 months of life and declined steeply over the first 5 years of life. Mean rates per 100000 in 2000-7 were 18.4, 27.6 and 464 for pneumococcal meningitis, bacteraemia and pneumonia, respectively, for children aged<2 years; 8.4, 14.9 and 295 for children aged<5 years (including those aged<2 years); and 2.2, 4.4 and 97 for children aged<20 years (including those aged<5 years). Mean rates per 100000 in 2006-7 for Sp. and NTHi otitis media combined were 631 (surgical) and 197 (medical) for children aged<2 years; 691 and 116 for children aged<5 years; and 281 and 35 for children aged<20 years. Pacific Island and indigenous Māori children generally had higher rates than European/other children. Rates increased with socioeconomic disadvantage, across all diagnoses. The annual cost to Government of pneumococcal disease and NTHi otitis media admissions for children aged<20 years was estimated at New Zealand dollars ($NZ)9.95 million (range 7.7-12.2 million) [about $US7.1 million]. Most of this cost was shared between pneumococcal pneumonia (48%) and otitis media (45%), and 78% was incurred in the first 2 years of life. Estimated annual paediatric mortality rates per 100 000 for children aged<5 years were 0.48, 0.30 and 0.54 for pneumococcal meningitis, bacteraemia and pneumonia, respectively. The analysis predicted four or five pneumococcal deaths per year (range 1-8) for children aged<5 years. Prior to the introduction of a national Sp. immunization programme, hospital admissions for Sp. disease and NTHi otitis media in NZ cost about $NZ10 million annually, mostly for children aged<2 years and particularly for those living in relative socioeconomic deprivation and for Pacific Island and Māori children. There were about five pneumococcal deaths annually. With adjustment for local serotypes, vaccine serotype coverage and uptake, immunization with any of the three available pneumococcal vaccines would reduce this burden substantially.