Introduction: African region is thought to contribute to >50% of deadly cases of pertussis worldwide, however surveillance and available data on Bordetella pertussis circulation are limited. Currently, pertussis vaccination schedule in most African countries is restricted to a primary immunization consisting of three doses during the first year of life using whole pertussis vaccines for which effectiveness is not known. Methods: Primary vaccinated children aged 3-15 years were recruited in Antananarivo city and suburban areas, Madagascar, and in Dapaong, Togo. Details on vaccine injections and a capillary serum sample were collected, and anti-pertussis toxin immunoglobulin G (anti-PT IgG) were quantified by ELISA. Results: Seropositivity rate was 56.9% (588/1033) and 62.2% (565/908) in Antananarivo and Dapaong, respectively. Significantly less children with anti-PT IgG were observed among those aged 3-5 years in Madagascar, seropositivity rate increased thereafter in children older ≥ 6 years old, with substantial sign of recent infection in particular in 6-8 years old children (18.9%; 39/206). In Dapaong, 65.3% (111/170) of the 3-5 years old children were seropositive and frequency did not significantly vary among age groups. Compliance was 89.0% (886/996) and 77.2% (596/772), and children vaccinated at age > 8 weeks represented 33.4% (337/996) and 39.4% (304/772) in Antananarivo and Dapaong, respectively. Compliance was higher among the 3-5 years children in both countries.