To study the epidemiology of pertussis in Greece and epidemiologic changes throughout a period of twenty-nine years, we conducted a retrospective analysis of available data of pertussis cases for the past twenty-nine years (1980–2008) and a prospective analysis of hospitalized pertussis cases from a children’s hospital in Athens for eight years (2001–2008). From 1980 through 2008, the incidence of pertussis in Greece declined from 11.2 to 0.05 cases per 100,000. Epidemic cycles occurring every 3 to 5 years were observed. Since pertussis circulation cannot be fully controlled by present immunization programs, efforts should be made to vaccinate infants at the recommended age, early diagnose, treatment as well as contact tracing of pertussis cases. Control of pertussis in social susceptible populations is necessary. A national program with adolescent and adult booster could decrease the circulation of B. pertussis. Despite an overall decrease for pertussis cases, pertussis is still a present and future challenge of public health service in Greece.