Accurate and timely diagnosis of pertussis continues to be challenging. The use of pertussis vaccine in Estonia since 1957 has dramatically altered the epidemiology and clinical presentation of pertussis disease. The clinical presentation in adolescents, adults and vaccinated children may be atypical without paroxysmal cough, posttussive vomiting and inspiratory whoop. Because of this, the diagnosis of pertussis should be confirmed with laboratory methods. Culture and PCR (polymerase chain reaction) may be used to identify Bordetella pertussis infection, but the sensitivity of these methods is high only in the early phase of the disease. Serologic tests are more useful for late diagnosis, but quantitative tests should be employed instead of qualitative tests.