Background: Nearly 10% of students enrolled in US public schools are absent daily. Although previous research has shown associations of school absenteeism with participation in risk behaviors, it is unclear if these associations vary by whether the absence was excused. The purpose of this study was to examine the associations of health risk behaviors with being absent from school with and without permission among high school students. Methods: During spring 2004, questionnaires similar to the Youth Risk Behavior Survey questionnaire were completed by 4517 ninth- and eleventh-grade students. Responses to items assessing frequency of school absences during the past 30 days for any reason and without permission were combined to create a variable coded as absent on: 0 days; greater than or equal 1 day, all with permission (WP); and greater than or equal 1 day, at least 1 day without permission (WOP). Logistic regression analyses controlling for gender, grade, and race/ethnicity examined the association of risk behaviors with absenteeism. Results: Controlling for demographic variables, compared to students who were absent 0 days, students who were absent WP had significantly higher odds of engaging in 25 of 55 risk behaviors examined and students who were absent WOP had significantly higher odds of engaging in 43 of the 55 behaviors. Students who were absent WOP also had approximately twice the odds of engaging in risk behaviors compared to students who were absent WP. Conclusions: School absenteeism, with and without permission, is associated with risk behaviors. Schools should recognize absenteeism for any reason as a warning sign for a variety of risk behaviors. (Contains 3 tables.)