We retrospectively analysed the incidence rate of reported cases of pertussis in Barcelona during 2009–2012 according to age, sex, type of medical centre and vaccination status. We included 748 confirmed or suspected cases, 613 (82.0 %) of which were confirmed by laboratory testing and the remaining 135 (18.0 %) by epidemiological evidence. The highest reported incidence of pertussis was amongst <1 year olds [96.1 per 100 000 person-years, 95 % confidence interval (CI): 84.3–109.1]. The majority of confirmed and suspected cases were reported in 2011 and 2012, and the total incidence (confirmed or suspected) was 6.3 (95 % CI: 5.6–6.9) and 4.2 (95 % CI: 3.6–4.7) per 100 000 person-years, respectively. Incidence increased significantly (P = 0.001) in 2011–2012 compared with 2009. Most confirmed cases occurred in children <1 year old (87.9 %). Cases were confirmed by real-time (RT)-PCR (87.5 %; 95 % CI: 81.3–87.6) and bacterial culture (13.7 %; 95 % CI: 11.0–17.1). We recommend performing RT-PCR in suspected cases with no epidemiological link to a confirmed case.