National estimates of injuries for children under 5 years based on population representative surveys are not readily available globally and have not been reported for developing countries. This study estimated the annual incidence, pattern and distribution of unintentional injuries according to age, gender, socio-economic status, urban/rural residence and disability caused among children aged under 5 years in Pakistan. The National Health Survey of Pakistan (NHSP 1990-94) is a nationally representative survey of households to assess the health profile of the country. A two-stage stratified design was used to select 3223 children under 5 years of age for interview and examination. Data were used for boys and girls in urban and rural areas over the preceding year. A community development index was developed to assess the relationship between socio-economic status and injuries. Weighted estimates were computed adjusting for complex survey design using surveyfreq and surveylogistic option of SAS 9.1 software. Post hoc power calculations were made for each variable keeping the design effect at 3.0. The overall annual incidence of unintentional injuries was 47.8 [95% CI 36.6, 59.0] per 1000 per year; 50.2 [95% CI 37.0, 63.4] and 45.2 [95% CI 29.4, 61.0] per 1000 per year among boys and girls under 5 years of age respectively. An estimated 1.1 million unintentional injuries occur in Pakistan annually among these children. Injury rates increase with age among the under-5s. Urban and rural injuries were 56.1 [95% CI 33.5, 78.7] and 44.1 [95% CI 31.1, 57.1] per 1000 per year respectively. The children living in least developed communities had almost 3 times higher risks of injuries than most developed communities. The annual incidence of types of injuries were: falls 28.7 [95% CI 19.5, 37.9], cuts/bruises 9.7 [95% CI 5.3, 14.1] and burns 6.6 [95% CI 3.0, 10.2] per 1000 per year. Falls were the most common type of injury (60%) followed by cuts/bruises (21%) and burns (14%). The majority of injuries occur at home (85%), with just 10% due to road traffic. Road traffic injuries and injuries to the female child were more likely to result in disability. There is a high burden of unintentional injuries and disability among children under 5 in Pakistan. These results are useful for planning further research and for prioritising prevention programmes nationally and in other developing countries with similar situation.