This paper describes the survey development, design and data collection protocol for the 2008/2009 Youth Smoking Survey (YSS) and the changes to the YSS survey and protocols across the 5 survey cycles (1994, 2002, 2004/2005, 2006/2007, 2008/2009). Canada's Youth Smoking Survey is a nationally representative school-based survey of students (grades 6 to 12 in 2008/2009) from randomly sampled public and private schools in the ten provinces. The main objective of the YSS is to provide benchmark data on national smoking prevalence rates for youth. Key features of the 2008/2009 YSS include consistent measures across survey cycles, a survey team of researchers and non-governmental organizations, a link to school and student level measures, provision of tailored feedback reports to schools and publicly available datasets.