There are no trend studies on various health risk behaviours among adolescents in Uruguay. Therefore, this study looked at trends in a number of health-risky behaviours among adolescents in Uruguay from three separate surveys. Data from 9272 adolescents (age range: 11-16 years), who took part in three cross-sectional national in-school surveys in Uruguay in 2006, 2012 and 2019 were analysed. A self-administered survey was used to evaluate 24 health risk behaviours. By using logistic regression analyses to treat the study year as a categorical variable and adjusting food insecurity and age, linear trends were examined. We found a significant increase in the prevalence of being overweight, having obesity, inadequate fruit intake, sedentary behaviour in leisure-time, physical inactivity, bullying victimisation, loneliness, suicidal ideation, and sexual activity. We found a significant decrease in current cigarette use, physical fighting and current alcohol use. Among males, a significant increase of non-condom use, and a decrease in current other tobacco use (other than cigarettes), being physically attacked and the number of sexual partners. Among females, we found an increase in food insecurity, trouble from alcohol use, multiple sexual partners, and sleep problems. Overall, from 2006 to 2019, there was a decrease in seven health risk behaviours among boys and/or girls. Among boys, there was an increase in 10 health risk behaviours and among girls, 15 health risk behaviours increased, highlighting adolescent girls' greater vulnerability, thereby perpetuating further gendered health inequalities. In Uruguay, school health programmes for adolescents are recommended.