In addition, blood markers linked to heart and metabolic risk factors were more prevalent in breakfast skippers and low-energy breakfast consumers than people who ate normal higher calorie breakfasts.
Lead researcher Dr Jose Penalvo from the Friedman School of Nutrition Science and Policy at Tufts University in the US, said: "Aside from the direct association with cardiovascular risk factors, skipping breakfast might serve as a marker for a general unhealthy diet or lifestyle which in turn is associated with the development and progression of atherosclerosis.
"Our findings are important for health professionals and might be used as a simple message for lifestyle-based interventions and public health strategies, as well as informing dietary recommendations and guidelines."
Participants who ignored breakfast had the largest waists and body mass indexes (BMIs) and highest levels of blood pressure, cholesterol and fasting blood sugar.
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They were also more likely to eat unhealthily, drink alcohol frequently, and smoke.
Rates of obesity and high blood pressure were greatest among breakfast skippers.
The scientists said they could not rule out reverse causation, with obese people skipping breakfast in order to lose weight.
The research appears in the Journal of the American College of Cardiology, whose editor-in-chief Dr Valentin Fuster was one of the authors.
Dr Fuster, director of the Mount Sinai Heart group of clinics in New York City, said: "People who regularly skip breakfast likely have an overall unhealthy lifestyle.
"This study provides evidence that this is one bad habit people can proactively change to reduce their risk for heart disease."