Objectives The aim of this study was to examine the association between oral health and health literacy, gender, age, family affluence and country of origin amongst adolescents from Slovakia and Poland, using data from the Health Behaviour in School-aged Children study. Methods We analysed data from the cross-sectional Health Behaviour in School-aged Children study conducted in 2022 on a representative sample of 6,289 Slovak and Polish 13- and 15-year old adolescents (mean age 14.48; SD = 1.01; 50.5% boys). Data was collected through self-administered online questionnaires completed by respondents in schools during classes. Binomial logistic regression models were used to assess associations between oral health and health literacy, gender, age, family affluence and country of origin amongst adolescents from Slovakia and Poland. Results The results indicate that boys (odds ratio/95% confidence interval OR/95% CI 0.431/0.381–0.489) are substantially less likely to engage in regular toothbrushing compared to girls, highlighting a persistent gender disparity in oral hygiene behaviour. Additionally, lower socioeconomic status, as measured by family affluence, is associated with a decreased likelihood of frequent toothbrushing (OR/95% CI 0.486/0.399–0.592 for low family affluence; OR/95% CI 0.761/0.647–0.895 for medium family affluence). Similarly, health literacy emerges as a key determinant, with adolescents exhibiting lower health literacy levels demonstrating significantly reduced engagement in regular toothbrushing (OR/95% CI 0.475/0.384–0.587 for low health literacy; OR/95% CI 0.666/0.550–0.808 for medium health literacy). Conclusion This study highlights the significant impact of gender, family affluence and health literacy on toothbrushing frequency amongst adolescents in Poland and Slovakia. The findings underscore the need for targeted oral health promotion strategies that consider gender differences, socioeconomic inequalities and the importance of health literacy in improving oral hygiene practises amongst adolescents.