Cardiovascular (CV) events have emerged as a major cause of morbidity and mortality among hematopoietic cell transplantation (HCT) survivors. Accumulating evidence supports the presence of increased CV risk in HCT recipients. Most studies have focused mainly on traditional CV risk factors, such as the metabolic syndrome and hypertension. However, detection of these factors suggests the development of irreversible overt clinical atherosclerosis. Therefore, earlier prediction of CV risk is needed to prevent CV morbidity and mortality in these patients. In the field of CV research, endothelial dysfunction is considered an early event in the pathophysiology of CV risk factors, and a number of markers have been proposed for its assessment. In addition, markers of subclinical target organ damage have been introduced to implement CV risk prediction and early preventive or intensive therapeutic interventions. Furthermore, a number of CV models have been suggested aiming for optimal stratification of patients. Preliminary studies have indicated excess CV risk using these early markers in HCT recipients. However, their role in the pathophysiology and clinical practice in HCT survivors remains largely understudied. Taking into account the need for increased awareness from treating physicians in this evolving setting, we conducted a state-of-the-art review aiming to summarize current knowledge on endothelial dysfunction, subclinical target organ damage, and CV risk prediction in HCT survivors.