Introduction: Electronic survey mode has become a more common tool of research than it used to be previously. This is strongly associated with the overall digitization of modern society. However, the evidence on the possible mode effect on study results has been scarce. Therefore, the aim of this study is to investigate the comparability of findings on health and behaviours using a paper-versus-electronic mode of survey with randomization design among schoolchildren. Methods: A randomized study was conducted using a mandatory questionnaire on international Health Behaviour in School-aged Children (HBSC) study in Lithuania, enrolling 531 schoolchildren aged 11–15 years. The questionnaire included health and social topics about physical activity, risk behaviours, self-reported health and symptoms, life satisfaction, bullying, fighting, family and school environment, peer relationships, electronic media communication, sociodemographic indicators, etc. The schoolchildren within classes were randomly selected for electronic or paper mode. Results: It was found that by study mode differences are inconsistent and in the majority of cases do not exceed 5%-point difference between the modes. The only significant difference was that in the paper survey the participants reported more exercise than in the electronic survey (OR=8.08, P<.001). Other trends were nonsignificant and did not show a consistent pattern – in certain behaviours the paper mode was related to healthier choices, while in others – the electronic. Conclusions: The use of electronic questionnaires in surveys of schoolchildren may provide findings that are comparable with concurrent or previously conducted paper surveys.