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Abstract Background Weight screening in schools has been proposed as one strategy to address childhood obesity. Students' response to such screening is unexplored, however. In this study we evaluated the perceived comfort, utility and impact of school-based weight screening from the perspective of middle school-aged students. Methods A cross-sectional study of 852 ethnically diverse 5th–8th grade students. Associations were investigated between measured height and weight screening data and responses to a self-administered questionnaire completed immediately following weight screening in physical education class. BMI categories were based on the revised 2000 CDC growth chart and definitions: 5th–85th BMI percentile = healthy weight, 85th–95th BMI percentile = at risk for overweight, and >95th percentile BMI = overweight. Results Overall, students' comfort level with weight screening varied depending on the student's own weight status. More overweight students (38.1%) reported being uncomfortable than healthy weight students (8.1%) (p < 0.001). In particular, overweight female students (54.8%) compared to healthy weight female students (21.6%) reported being uncomfortable (p < 0.01). About half (54.9%) of all students reported knowing their weight prior to screening, and 58.9% reported that it was useful to learn their height and weight. Compared to healthy weight students, overweight students were significantly more likely to report the intention to perform weight modification related activities such as visiting a doctor (Odds ratio (OR) = 2.0, 95% CI = 1.3, 3.1), eating more fruits and vegetables (OR = 2.7, 95% CI = 1.7, 4.1), and increasing physical activity (OR = 4.3, 95% CI = 2.7, 7.0). Conclusion Overall, the majority of the middle school students did not report discomfort with school-based weight screening, did report that receiving height and weight information was useful, and generally report appropriate weight control intentions. These proportions varied across weight status categories, however, with students who were at risk for overweight or overweight reporting higher levels of discomfort. For schools that conduct weight screening, it is essential that they also provide comfortable and private settings as well as education or counseling regarding healthy weight control practices.