Thrombosis is a serious complication of heart failure for which available data on pediatric patients are scarce. This report describes the frequency and risk factors of clinically significant thrombosis (CST) for children awaiting transplantation. A retrospective study analyzed a cohort of heart recipients with CST, defined by the presence of intracardiac thrombus by imaging, explant pathology, or symptomatic clinical event. Among the 123 patients in the study, 56 % were male and 44 % had congenital heart disease. The median age at transplantation was 6.6 years (range 0-30 years). The prevalence of CST was 12.2 % (15/123), and its incidence was 32.7 events per 100 patient-years. The thromboembolic event frequencies were 2.4 % and 6.5 events per 100 patient-years. The median interval from listing to CST was eight days (range 0-113 days). The median wait-list duration was 31 days (range 8-169 days) in the CST group versus 51 days (range 0-1,743 days) in the non-CST group. Inpatient status was statistically associated with CST (14 of 15 subjects were inpatients, p = 0.03). Inotropic support (p = 0.068) and United Network for Organ Sharing (UNOS) status 1 (p = 0.061) approached significance. Clinically significant thrombosis was common in this end-stage heart failure population. Until randomized clinical trial data are available, it may be reasonable to consider anticoagulation for children admitted with decompensated heart failure and listed as UNOS status 1.