Colonization of the upper respiratory tract with Streptococcus pneumoniae is the precursor of pneumococcal pneumonia and invasive disease. Following exposure, however, it is unclear which human immune mechanisms determine whether a pathogen will colonize. We used a human challenge model to investigate host-pathogen interactions in the first hours and days following intranasal exposure to Streptococcus pneumoniae. Using a novel home sampling method, we measured early immune responses and bacterial density dynamics in the nose and saliva after pneumococcal exposure. We found that nasal colonization can take up to 24 hours to become established. Also, two distinct bacterial clearance profiles were associated with protection: nasal clearers with immediate clearance of bacteria in the nose by the activity of pre-existent mucosal neutrophils and saliva clearers with detectable pneumococcus in saliva at one-hour post challenge and delayed clearance mediated by an inflammatory response and increased neutrophil activity 24 hours post bacterial encounter.The human respiratory tract is a major site of contact with aerosolised bacteria. Acute respiratory tract infections are common, and pneumonia causes more than 1.3 million child deaths annually 1,2 ; as well as frequent hospitalisations in at-risk groups such as the elderly, people with chronic lung disease and asthmatics 3 .The first stage of such infections is the successful colonization of the upper respiratory tract by the pathogen 4 . Streptococcus pneumoniae (Spn), the major bacterial cause of pneumonia, inhabits the nasopharynx of 40-95% of infants and 10-25% of adults without causing disease 5 .Colonization is usually asymptomatic in adults but can be associated with mild rhinitis symptoms in children 6 . Different serotypes of pneumococcus may inhabit the nasopharynx at varying densities 7,8 , which is especially common in children 9 . Colonization may continue for a period of weeks or months and be eliminated and reacquired many times during lifetime 10 .As pneumococcal colonization is the primary reservoir for transmission 11 and a prerequisite of invasive disease 12 , its control is key to preventing disease. Importantly, the determinants of whether exposure to a bacterium leads to colonization have not been identified.Epidemiological studies and pre-clinical studies with animal models point to factors such as host age, immune status, virus co-infection, exposure to antibiotics, smoking and overcrowded living conditions 13,14,15 . However, evidence from in vivo human studies is lacking.Our well-established Experimental Human Pneumococcal Challenge (EHPC) model allows for the rapid, safe and accurate study of bacterial encounter at the nasopharynx in humans 16 .The precise dose and timing of infection are known. Individuals are inoculated with live type 6B pneumococcus and pneumococcal colonization (detection and density), is assessed by nasal washes collected from 48 hours onwards post-exposure. After this point, approximately