Management of symptoms and prevention of life-threatening haemorrhage in Immune thrombocytopenia (ITP) must be balanced against adverse effects of available therapies. Since current treatment guidelines based on platelet count are confounded by variable bleeding phenotypes, there is a need to identify new objective markers of disease severity for improved treatment stratification. In this cross-sectional, prospective study of 49 patients with ITP and lowest recorded (nadir) platelet counts below 30 x 109/L, we used Susceptibility-Weighted Magnetic Resonance Imaging (SWI) to detect cerebral microbleeds (CMBs) as a marker of occult haemorrhage. CMBs were detected using a semi-automated method and correlated with clinical metadata using multivariate Poisson regression analysis. Lobar CMBs were identified in 43% (21/49); prevalence increased with decreasing nadir platelet count (15/25 <5x109/L; 4/11 5-9x109/L; 2/9 10-14x109/L; 0/4 >15x109/L), and was associated with longer disease duration (p=7x10-6), lower nadir platelet count (p=0.005), lower platelet count at time of MRI (p=0.029), and higher organ bleeding scores (p=0.028). Mucosal and skin bleeding scores, number of previous treatments, age and sex were not associated with CMBs. Occult cerebral microhaemorrhage is common in patients with moderate to severe ITP. Strong associations with ITP duration may reflect CMB accrual over time or more refractory disease. Although associated, neither low platelet count or bleeding scores predict CMBs. SWI could therefore provide an additional non-invasive biomarker of haemorrhagic phenotype, and potential adjunct for treatment stratification. Further longitudinal studies in children and adults will allow greater understanding of the natural history, and clinical and prognostic significance of CMBs.