This study examines different factors influencing the 13-valent pneumococcal conjugate vaccine (PCV13) specific antibody response in 8-13 months old Danish children starting in day care. We present secondary findings to the ProbiComp study, which included nose swabs, buccal swabs and blood samples from the children before entering day care (baseline) and again after 6 months. Pneumococci isolated from nose swabs were identified by latex agglutination kit and Quellung reaction. Luminexbased assay was used for antibody measurements against specific anti-pneumococcal capsular IgG. Buccal gene expression was analyzed by qPCR. Statistical analyses were performed in R and included Pearson's Chi-squared test, Welch two sample t-test and linear regression models. The PCV13 antibody response was unaffected by whether the children were carriers or non-carriers of any pneumococcal serotype. Having siblings increased the risk of carrying serotype 21 before day care (p = 0.020), and having siblings increased the PCV13 antibody response at the end of study (p = 0.0135). Hepatitis B-vaccination increased the PCV13 antibody response before day care attendance (p = 0.005). The expression of IL8 and IL1B was higher in children carrying any pneumococcal serotype at baseline compared to non-carriers (p = 0.0125 and p = 0.0268 respectively). Invasive pneumococcal disease (IPD) caused by Streptococcus pneumoniae (S. pneumoniae) is associated with high mortality and morbidity worldwide, especially among elderly aged 65+ years old and young children <2 years of age 1. More than 92 different serotypes of S. pneumoniae are known 2 and the 13-valent pneumococcal conjugate vaccine (PCV13), which was introduced into the Danish Childhood Immunization Program in 2010, protects against 13 of the known serotypes (