Background & aim: Congenital heart disease is one of the most common malformations at birth that require timely recognition and treatment. The aim of this study was to determine the prevalence and etiology of detected heart murmurs and association between congenital heart disease and heart murmurs. Recognition of murmurs etiology would help us to manage and treat them properly. Methods: In this cross-sectional study, 2757 infants between two to 24 months in Kerman city, Iran were enrolled. The infants who had heart murmurs in physical exam were referred to pediatric cardiologist for more evaluations such as echocardiography. Results: 2757 infants were screened for the presence of heart murmurs and murmurs were heard in 145 (5.29%) including 71 girls (49%) and 74 boys (51%). Innocent and pathologic murmurs prevalence was 49 and 51 percent, respectively. Altogether, left to right shunts [ventricular ceptal defect (VSD), atrial ceptal defect (ASD), patent ductus arteriosus (PDA), atrioventricular septal defect (AVSD)] were the most common cardiac abnormalities in this study. The most common heart lesion was ventricular septal defect (21.6%). There was a significant correlation between younger infants, lower weights and girl sex with congenital heart disease. Conclusion: On base of our study, the incidence of pathologic heart murmurs related to congenital heart disease is more than innocent murmurs in infants; with accurate heart exam and timely screening, we can prevent irreversible heart complication in these ages