Myeloproliferative disorders (MPD) are associated with an increased risk for thrombembolic events. In this study, we examined the prognostic value of transcranial Doppler (TCD) microemboli detection regarding clinical events and correlated TCD findings with results of blood cell counts and platelet flow cytometry to gain insight into the composition of circulating microemboli in these patients. In a cohort of 42 patients with MPD TCD microemboli detection was performed on a single occasion and correlated with thrombembolic events during a prospective follow up of 29.7 ± 7.3 month. In all patients, a complete blood count and in 17 patients platelet flow cytometry were performed on the day of the TCD examination. Microembolic signals (MES) were recorded in 15 (35.7%) patients, however, without any correlation with the type of MPD, blood cell counts, or thrombembolic events [9 (21.4%)]. MES positive and negative patients did not differ regarding the levels of activated platelets, platelet microaggregates, or microparticles. We found a strong trend for higher rates of platelet–neutrophil conjugates in MES positive patients (P = 0.09). Detection of MES by TCD on a single occasion in MPD patients has only limited prognostic value. MES do not correlate with the type of MPD, nor blood cell counts. Flow cytometry suggests that MES in MPD may consist of platelet–neutrophil aggregates.