Administrative databases can be a reliable source for estimating the epidemiology of blood disorders. No data are available estimating the epidemiology of thrombocytopenia from administrative data in Italian institutions. We analyzed the administrative database of the Padua University Hospital with the aim to study the epidemiology of thrombocytopenia in patients discharged with an International Classification of Disease, 9th Revision, Clinical Modification (ICD9-CM) code of thrombocytopenia. The database from year 2004 to 2008 was evaluated and all cases of thrombocytopenia (Code 287.1, 3, 4, 5) were identified and analyzed with regard to age, sex, associated diseases, therapeutics procedures and bleeding complications. The accuracy of electronic records was validated in all available medical records of patients discharged in 2009, by applying the ICD9-CM update 2007 version (Code 287.1, 4, 5; 287.30, 31, 32, 33, 39). We found 368 patients discharged from 2004 to 2008 with an ICD9-CM code of thrombocytopenia, correspondent to 0.1% of discharge rate and to a rate of 73.6 patients/year. The incidence of thrombocytopenia for this period was 14.8 cases per 100,000 per year. When considering patients with an ICD9-CM diagnosis of immune thrombocytopenia (ITP: Code 287.3), the incidence was of 6.8 cases per 100,000 per year. The clinical records of 40 patients with a discharge diagnosis of thrombocytopenia during year 2009 were reviewed for clinical consistency with ICD9-CM codes. A concordant diagnosis between clinical records and discharge code was found in 82.5% of cases. Following validation of ICD9-CM code, the incidence of ITP (Code 287.31) was 2.6 cases per 100,000 per year. When evaluated for sensitivity and specificity, we found the ICD-9-CM to be useful in studying thrombocytopenia using administrative data.