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.