Coronary artery calcification is an early marker of subclinical atherosclerosis, but little research has been done in asymptomatic individuals under 45 years. In this cohort study with 17 years of follow-up, 155 participants were assessed in 2016 with a coronary calcium score for the association with cardiovascular risk factors. During follow-up, there was a significant increase in anthropometric measurements, cholesterol and fractions, and diastolic pressure. Participants who gained 1 cm in waist circumference had a mean reduction of 0.36 mg/dL in HDL-cholesterol and those who gained 1 kg/m2 in body mass index had a reduction of 0.72 mg/dL in HDL-cholesterol. Married participants had a 4.78 mg/dL reduction in HDL-cholesterol levels compared to singles. There was an increase of 2.09 mg/dL in HDL-cholesterol at each higher level of self-perceived health. One single case, a 32-year-old male, smoker, sedentary individual with a family history of cardiovascular disease, presented coronary calcification (0.6%). His HDL-cholesterol was reduced by 43.4%, with levels of less than 25 mg/dL at the time of coronary calcium scoring. Our findings may prompt broader studies of populations under 35 years with HDL-C levels below 25 mg/dL and family histories of cardiovascular disease, associated with obesity, sedentary lifestyle and smoking.