BACKGROUND: Whooping cough is a communicable disease whose incidence has increased in recent years in some countries with vaccination. Since 1981, in Catalonia (Spain), cases must be reported to the Public Health Department. In 1997, surveillance changed from aggregated counts to individual report and the surveillance system was improved after 2002. Catalan public health is universal with equal coverage geographically. The aim of this study was to determine whether there are differences in whooping cough incidence in rural and urban counties. METHODS: Cases in 1990-2010 were classified as rural or urban. Incidences and risk ratios (RR) between urban and rural counties and 95% CI were calculated. Associations between rural and urban counties and structural changes during the study period were analysed. RESULTS: Twelve years of the whole study period showed differences in incidence between rural and urban counties. The incidence was higher in urban counties in seven years and rural counties in five years. There was a positive association of whooping cough incidence in rural and urban counties in four-week periods. Structural changes were detected in the following four-week periods: 4th in 1993, 7th in 1996 and 3rd 2005 in rural counties and 5th 1993, 9th in 1996 and 8th in 2007 in urban counties. CONCLUSIONS: Differences in whooping cough between rural and urban counties were found. In most years, the incidence was higher in urban than in rural counties. Rural and urban counties show similar cyclic behaviour when four-week periods were considered.