The aims of this study were to estimate influenza vaccination coverage for children during the 2006-2007 influenza season in Ontario, Canada, where universal vaccination is available, and to compare the rate among children aged 6-23 months with corresponding rates from other Canadian provinces that specifically target this high-risk group. We conducted a telephone survey of caregivers of children aged 6 months-11 years that included 4854 children from 3029 households. Ontario's vaccination rate (complete and partial coverage combined) for children aged 2-11 years was 28.3% (95% CI 26.3-30.5%) for healthy children and 36.8% (95% CI 31.4-42.5%) for those with chronic conditions. Immunization coverage of children aged 6-23 months was 24.0% (95% CI 20.6-27.7%) in Ontario, similar to Manitoba's rate of 24.1% but lower than rates in other provinces: Nova Scotia (35.5%), Quebec (41.8% for 1 year olds and 37.7% for 2 year olds during the 2005-2006 season), Saskatchewan (32.5%) and Alberta (52.2%). Universal vaccination in Ontario has achieved modest coverage in children aged 2-11 years, but has been less successful than targeted programs in vaccinating infants aged 6-23 months.