BackgroundStudies reporting the natural immune responses against malaria in children from different geographical settings in endemic areas are not readily available. This study was aimed at comparing the immune responses against Plasmodium falciparum MSP-119 antigen in children from five contrasting bioecological zones in Cameroon.MethodsIn a cross-sectional survey, children between 2 and 15 years, were enrolled from five ecological strata including the south Cameroonian equatorial forest, sudano-sahelian, high inland plateau, high western plateau, and the coastal strata. The children were screened for clinical malaria (defined by malaria parasitaemia ≥ 5000 parasites/µl plus axillary temperature ≥ 37.5 °C). Their antibody responses were measured against P. falciparum MSP-119 antigen using standard ELISA technique.ResultsIn all, 415 children comprising 217 (52.3%) males participated. Total IgG and IgG1–IgG4 titres were observed to increase with age in all the strata except in the sudano-sahelian and high inland plateau strata. Total IgG and IgG1–IgG4 titres were significantly higher in the coastal strata and lowest in the high inland plateau (for IgG1 and IgG2) and sudano-sahelian strata (for IgG3 and IgG4). Titres of the cytophilic antibodies (IgG1 and IgG3) were significantly higher than the non-cytophilic antibodies (IgG2 and IgG4) in all the strata except in the sudano-sahelian and high inland plateau strata. Total IgG and IgG subclass titres were significantly higher in children positive for clinical malaria compared to negative children in all study sites except in the high western plateau and coastal (for IgG1 and IgG3), and the sudano-sahelian strata (for all antibodies). Furthermore, a significant positive correlation was observed between parasite density and IgG2 or IgG4 titres in all study sites except in the south Cameroonian equatorial forest and sudano-sahelian strata.ConclusionsThis study showed that antibody responses against MSP-119 vary considerably in children from the different bioecological strata in Cameroon and could be linked to the differential exposure to malaria in the different strata. Furthermore, the rate of antibody acquisition was not observed to increase in an age-dependent manner in low transmission settings.Electronic supplementary materialThe online version of this article (10.1186/s12936-019-2654-9) contains supplementary material, which is available to authorized users.