The External Quality Assurance (EQA) in medical microbiology in the Czech Republic is well organized. It is coordinated by the Accreditation Department of the Centre of Epidemiology and Microbiology (AD-CEM) of the National Institute of Public Health in Prague. Since 1993 when the first samples were sent out the number of programmes and participating laboratories has been rapidly increasing. EQA for Human papillomavirus (HPV) has been available since 2000. As has been shown for other programmes, the EQA for HPV has proved to be useful, helping to improve the accuracy of analyses and contributing to the standardization of methods of HPV DNA testing. EQA for HPV has been well received by routine laboratories, demonstrated by a high number of these institutions voluntarily participating in EQA.