Fetomaternal alloimmune thrombocytopenia (FMAIT) is the most common cause of severe neonatal thrombocytopenia in otherwise well, term infants. First pregnancies are often severely affected. This descriptive, population-based national study was undertaken in order to inform the case for antenatal screening. Cases were identified using three sources and capture-recapture techniques used to generate a robust incidence estimate. One hundred and seventy three cases were identified between October 2006 and September 2008. An extra 20 cases were estimated from capture-recapture analysis, giving an estimated incidence of clinically detected FMAIT of 12·4 cases per 100 000 total births (95%confidence interval: 10·7, 14·3). Fifty-two cases (30%) were known at the start of pregnancy; 120 (70%) were unknown (n = 115) or unrecognized (n = 5). Unknown cases were more likely to experience a haemorrhagic complication (67% vs. 5%) (P < 0·001) and more likely to have an intracranial haemorrhage (20% vs. 4%) (P = 0·014) than known cases receiving antenatal management. In view of the incidence of severe disease identified, further assessment of the case for antenatal screening is important. There were a number of cases in which the significance of a history of FMAIT in a previous sibling was not recognized and there is a need to raise awareness of the importance of this diagnosis.