The aim of the study was to investigate the association of chronotype categories with type 2 diabetes mellitus (T2DM) and cardiovascular diseases (CVD) in 172 middle-aged adults (71.5% females; 51.8 ± 15.7 years). Anthropometric parameters, lifestyle habits, adherence to the Mediterranean Diet (MD), sleep quality, chronotype and the presence of T2DM and CVD were studied. Chronotype was classified as morning in 58.1% of subjects, evening in 12.8% and intermediate in 28.1%. Subjects with evening chronotype followed an unhealthier lifestyle than other chronotypes; indeed, they significantly performed less regular activity and were more frequently smokers. Furthermore, they had significantly higher risk to have T2DM [Odds Ratio (OR)=3.36 95% confidence interval (CI) 1.14-35.42; p = 0.03] and CVD [Odds Ratio (OR)= 5.89 95% CI 1.14-30.60; p = 0.035](CI) 2.24-407.54); p = 0.01] compared to morning chronotype after adjustment for gender, body mass index (BMI), sleep quality and adherence to the MD. The confidence intervals were wide, indicating that the sample size was too small. Thus, these data need to be replicated in a larger sample size. In addition, nutritional assessment was limited since only PREDIMED questionnaire was carried out. However, the main strengths of this study included a random sample and a population-based approach, although the cross-sectional design cannot establish causality. Although study population was unbalanced per gender and smoking and age group representing only middle-aged people,we adjusted the statistical analysis for potential confounding factors. In conclusion, the evening chronotype has an increased risk to be associated to T2DM and CVD.