Background: Thrombocytopenia is an immune-mediated disease, which affects suckling piglets. Piglets are pale and inactive, show multiple hemorrhages and often die within days. Pathological examination reveals severe haemorrhages and oedema in several organs. Severe thrombocytopenia and elongated bleeding time characterize the disease haematologically. The sow produces antibodies against the thrombocyte antigens of the boar, which are present in the blood of the piglets. These isoimmune antibodies attack the platelets and megakaryocytes of the piglets, causing thrombocytopenia in succeeding matings of the same boar and sow. There is no known therapy against this condition. In the last few decades, the disease has become rare due to the increase of artificial insemination. Case presentation: On an organic breeding farm in Switzerland with a high percentage of natural pen matings, piglets of three litters showed haemorrhages on the skin, prolonged bleeding time and were generally in a reduced general state. A pathological examination revealed multifocal haemorrhages in the stomach, kidneys, dermis, mesenterium and spinal cord. Haematology showed a massive thrombocytopenia and regenerative anaemia. Due to these findings the diagnosis of thrombocytopenic purpura was established. To avoid further matings of the same boar and sow and thus more affected piglets, out of three possible boars the responsible sire had to be determined. This was achieved through array genotyping and subsequent computation of identity by descent and calculation of Mendelian errors for parentage verification. Thereby the responsible boar was identified and as a consequence removed from the farm. Further preventive measures, that had been established, included the recording of all matings and regular exchange of boars. Conclusion: The decreased number of natural matings with the surge of artificial insemination has probably reduced the number of cases of thrombocytopenic purpura and thus the disease awareness of farmers and veterinarians. However, as consumers wish for better animal welfare and higher ecological standards we may see a rise in natural matings and thus a return of the disease. In case of affected litters, genetic testing was proven a valid method for investigation and prevention of more cases and may be used more in the future.