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Objectives Unhealthy habits acquired during adolescence may persist in adulthood and eventually increase the risk of chronic illnesses. Study design We reported on a survey conducted in 2013–2015 among secondary school students in Tuscany, central Italy. Methods We compared the prevalence of self-reported lifestyle characteristics and overweight/obesity between genders and age groups (14–16 vs 17–21 years). We partitioned each gender- and age-specific stratum into groups based on cigarette smoking and engagement in sport activities, and compared the prevalence of other unhealthy lifestyles across groups using Poisson regression. Results Overall, 2167 students (53.3% males, mean age 16.8 years) were included. Males were more frequently overweight/obese than females. Cigarette smoking increased with age and did not differ by gender. Males were more likely to engage in sport activities, drink alcoholic beverages and adopt other unhealthy lifestyle habits, whereas females reported a more frequent use of painkillers. Cigarette smoking was the single lifestyle characteristic most consistently associated with other unhealthy habits. Conclusions The prevalence and patterns of co-occurrence of unhealthy lifestyle habits varied by gender and age group among secondary school students in Italy. Our findings should be taken into account when planning public health initiatives aiming to combat obesity and tackle unhealthy lifestyles among secondary school students in Italy.