Individuals with Prader–Willi syndrome (PWS) may be at higher risk of developing blood clots as compared to the typical population, but this risk is poorly understood. It is also unclear if laboratory testing of D-dimer concentration might be useful to screen for thrombosis in PWS. Here, we surveyed the thrombosis history of 883 individuals with PWS and evaluated the D-dimer concentration in a subset of 214 asymptomatic individuals, ages 5–55. A history of at least one blood clot was reported by 3.6% of respondents. Thrombosis increased with age, but no significant difference was found on the basis of sex or family history. Genetic subtype was a significant factor when considering only those with a known subtype, and individuals with a history of edema had significantly more blood clots. In the D-dimer sub-study, ≈15% of participants had high D-dimer concentrations, and 3.7% had D-dimer values more than twice the normal upper limit. One participant with a high D-dimer result was found to have a blood clot. No significant differences in D-dimer results were found on the basis of age, sex, genetic subtype, family history of blood clots, edema history, or BMI. The D-dimer test does not appear to be a sensitive and specific screening tool for blood clots in asymptomatic individuals with PWS.