We aimed to investigate transmission rates of pertussis in household contacts of cases and factors associated with transmission. A prospective epidemiological study was conducted in 2012 and 2013 to determine the incidence of pertussis among household contacts of reported cases in Catalonia and Navarre, Spain. An epidemiological survey was completed for each case and contact, who were followed for 28 days to determine the source of infection (primary case) and detect the occurrence of secondary cases. Odds ratios (ORs) were used to estimate the effectiveness of vaccination and chemoprophylaxis in preventing new cases, using the formula (1 - OR) × 100. For the 688 primary cases, a total of 2,852 contacts were recorded. The household transmission rate was 16.1% (459/2,852) and rose according to the age (> 18 years) and lack of immunisation of the primary cases, and also the age (0-18 years), family relationship (siblings and children), lack of vaccination and chemoprophylaxis of contacts. Pertussis vaccine effectiveness in preventing new cases was 65.0% (95% confidence interval (CI): 11.6 to 86.2) for full vaccination (≥ 4 doses) and 59.7% (95% CI: -6.8 to 84.8) for incomplete vaccination (< 4 doses). The effectiveness of chemoprophylaxis was 62.1% (95% CI: 40.3 to 75.9). To reduce household transmission, contacts should be investigated to detect further cases and to administer chemoprophylaxis. The current vaccination status of cases and contacts can reduce household transmission.