Today the need to analyze health behaviour from a gender perspective is as imminent as ever, particularly at university, where the number of women who register is on the rise and has exceeded the number of male students worldwide. We carried out a prevalence study aimed at analyzing Spanish university students' lifestyles and identify differences according to gender and academic discipline. Of 3,646 eligible subjects doing university courses related to health (Group A), education (Group B) and other professions (Group C), 985 (27.0%) participated in the study. Information was elicited about their physical activity level, disturbed eating attitudes, consumption of alcohol, tobacco and illegal substances. Prevalence and Odds Ratios (OR) were calculated according to sex and kind of academic discipline. The obtained data confirmed that only 27.4% of the students were considered as sufficiently active, while 14.9% of them suffered from disturbed eating attitudes (DEA). Women were particularly less active (OR 0.46 (0.32-0.66); p < 0.0001), and more sedentary than men (OR 1.40 (1.00-1.97); p = 0.03). Binge drinking was more frequent in female than in male students (OR 1.79 (1.29-2.47); p = 0.0004). A third of the analyzed sample admitted that they had used illegal substances, while a lower consumption prevalence was found in women (OR 0.53 (0.40-0.71); p < 0.0001). The studied population was not very active (27.4%), especially women (OR = 0.45). Therefore, it seems that Spanish university students lead an unhealthy lifestyle, a situation which seems more conspicuous amongst females.