Cardiovascular diseases are among the leading causes of death worldwide. Lack of accurate estimation of the risk factors associated with these diseases can impair the designing of effective interventions in this field; the present study aimed to investigate the risk factors attributable to cardiovascular diseases in males and females visiting comprehensive health service centers in 2018. This cross-sectional study is part of the national health transformation plan shaped in response to the emerging epidemic of noncommunicable diseases. In the present study, 6,331 participants aged 30 years and older were randomly and census selected from comprehensive urban and rural health service centers in Naein County, in Isfahan, Iran, respectively. The data were collected using the electronic health record from the IraPEN program in two sections: demographic information and the prevalence of cardiovascular disease risk factors. They were then analyzed with Statistical Package for the Social Sciences (SPSS) 24 software using descriptive statistics, Chi-square test, one-way ANOVA, and logistic regression. The participants' mean age was 55.09 ± 16.11 years. The main risk factor was insufficient consumption of fruits and vegetables while smoking was a negligible risk factor. Low physical activity, diabetes, hypertension, hypercholesterolemia, and high body mass index were more prevalent in females than in males, whereas smoking was more frequently reported in males (P < 0.001). Risk factors such as age, gender, education level, place of residence, and marital status, played a significant role in determining CVD risk factors. More than half of Iranian adults had one or older cardiovascular disease-related risk factors, and the prevalence of such factors was higher in females than in males. Given the importance of gender differences in cardiovascular disease-related health habits, it is necessary to reduce the majority of these diseases in society, especially in women, by controlling modifiable risk factors.