Background To mitigate the burden of pneumococcal infections in Niger, a 13-valent pneumococcal vaccine, PCV13, was introduced for routine child vaccination in July 2014. In order to provide pre-vaccine baseline data and allow appreciation of changes on carriage due to vaccination, we analyzed retrospectively pneumococcal isolates obtained from healthy, 0 to 2 year old children prior to the vaccine introduction. Methods From June 5, 2007, to May 26, 2008,1200 nasopharyngeal swabs were collected from healthy 0 to 2 year old children and analyzed by standard microbiological methods. Serotyping was done by SM-PCR and the data were analyzed with R version 2.15.0 (2012-03-30). Results Streptococcus pneumoniae was detected in 654/1200 children (54.5%) among whom 339 (51.8%) were males. The ages of the study subjects varied from few days to 26 months (mean = 7.1, median = 6, 95% CI [6.8-7.4]). Out of 654 frozen isolates, 377 (54.8%) were able to be re-grown and analyzed. In total, 32 different serogroups/serotypes were detected of which, the most prevalent were 6/(6A/6B/6C/6D) (15.6%), 23F (10.6%), 19F (9.3%), 14 (9%), 19A (5.6%), 23B (4.0%), 25F/38 (3.7%), 18/(18A/18B/18C/18F) (2.9%) and PCR non-typeable (16.4%). Eleven serogroups/serotypes accounting for 57.3% (216/377) were of PCV13 types. Of the 211/377 (56%) isolates tested for drug sensitivity, 23/211 (10.9%), 24/211 (11.4%), 9/211(4.3%) and 148/210 (70.5%) were respectively resistance to oxacillin, chloramphenicol, erythromycin and tetracycline. Thirteen of the oxacillin resistant isolates were additionally multidrug-resistant. No resistance was however detected to gentamy-cin500μg and to fluoroquinolones (ø Norfloxacin5μg 3 months and presence in family of more than one sibling aged 3 months and presence in family of children aged 0.5μg (CA-SFM, 2013 edition). All data collected have been confidentially recorded into a MySQL database and extracted to Excel for analysis with open source R v.2.15.0 (2012-03-30); The R Foundation for Statistical Computing, ISBN 3-900051-07 0. X2 test was used to compare frequencies or means. Risk factors for SPN carriage were first analyzed individually by univariate (single variable) analysis then examined together in multivariable (multiple variables) analysis by logistic regression model. The study was conducted in accordance with the then last Helsinki Declaration and started after approval obtained from the Niger National Consultative Committee of Ethic through deliberation N° 02/2007/CCNE of February1, 2007. Detailed information about the study aim, the sampling method and its related risk, the use and confidentiality of data were all made clear to parents or to next of kin before obtaining and signing their consent. Parents or next of kin were free to refuse the participation of their child, to ask question or to have access to the laboratory result when they wished. Sample collection, analysis and waste management were carried out according to WHO recommendations[12]