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Little is known about relation of overall breakfast quality with cardiometabolic risk factors. Therefore, this study aimed to explore sex-specific associations between breakfast quality and cardiometabolic risk profiles in a sample of an upper middle-aged German population.Cardiometabolic profiles of 339 men and 329 women were cross-sectionally assessed using an overall biomarker score (BScore), glycated hemoglobin (HbA1c), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), triglycerides (TG), blood pressure, body mass index (BMI) and waist circumference (WC). Overall breakfast quality was assessed by using (i) an a-priori defined breakfast quality score (BQS) and (ii) data-driven breakfast patterns based on principal component analysis (PCA). Multiple linear regression models for association of breakfast quality with all outcomes were adjusted for all potential confounders including overall diet quality.After adjustment for all potential confounders the BQS was inversely associated with the BScore (regression beta with 95% Confidence Interval: − 0.29 (052 − 0.06)) and HbA1c (−0.12 (−0.21, − 0.04)) in men; whereas no such associations were observed in women. Four breakfast (B) patterns were identified: B-processed-food pattern, B-cereal pattern, B-high fat pattern and B-dairy & cereal pattern. The B-processed-food pattern was positively associated with HbA1c (0.09(0.01, 0.18)), BMI (0.16 (0.06, 0.26)), and WC (0.17 (0.8, 0.26)) in men, and BMI (0.13 (0.1, 0.25)) and WC (0.11(0.01.0.22)) in women. The B-cereal pattern was inversely associated with BScore (−0.23 (−0.45, − 0.01)) and BMI (−0.11 (−0.20, − 0.01)) in men and WC(−0.16 (−0.27, − 0.05)) in women. The B-dairy & cereal pattern was also inversely associated with BScore (−0.26 (−0.48, − 0.04)) in men but not in women.The overall breakfast quality was cross-sectionally associated with a healthier cardiometabolic profile, especially in upper-middle age men, independent of overall dietary quality. Such analyses should be supplemented by studies investigating the circadian sequence of food intake and metabolic consequences including hard disease endpoints.