The aim of this study was to investigate the presence of cardiovascular and metabolic syndrome (MetSyn) risk factors in adolescents and University students in Crete (Greece), according to different levels of snack consumption. 237 adolescents (14.2-16.3 years) and 196 University students (19.5-31.5 years) participated during 2002/3 and 2004/5. Dietary intake (24-h dietary recalls), cardiorespiratory fitness, smoking habits, time spent watching television, anthropometric, blood pressure and biochemical measurements were assessed in all subjects. Adolescents consumed snacks more often than University students (62% vs. 49.5%, P <0.05) and had significantly higher total energy intake (8629 vs. 7641 kJ, P <0.05) and energy intake from snacks (2537 vs. 1767 kJ, P <0.001). Snack consumers had higher energy intake than non-consumers in both groups. No relationship was found between snack consumption and MetSyn risk factors, cardiorespiratory fitness and smoking. However, University students who consumed snacks had 15.36 times higher risk of having ≥ 2 MetSyn risk factors than adolescent snack consumers, had considerably higher LDL-cholesterol levels, total: HDL-cholesterol ratio and watched more television than non-consumers. These findings emphasize the need for developing effective nutrition interventions to promote healthier snack choices in adolescents and young adults with characteristics similar to our sample, in order to prevent cardiovascular risk later in adulthood.