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Streptococcus pneumoniae is the most frequent bacterial cause of morbidity and mortality in young children. Bacteria carried in the nasopharynx of healthy children reflect the prevalent strains circulating in the community.We recruited 464 newborns from a rural area in South India with endemic vitamin A deficiency. Nasopharyngeal specimens were collected from each infant at ages 2, 4 and 6 months.Fifty-four percent of study infants were colonized by age 2 months, with 64.1 and 70.2% carriage prevalence at ages 4 and 6 months, respectively. The odds of carriage at 2 months were significantly increased in female infants, infants living in a household in which 20 or more cigarettes were smoked each day, infants whose mothers had less than 1 year of schooling and infants fed colostrum. At age 4 months infants having 2 or more siblings <5 years of age were at significantly increased risk of carriage. At age 6 months none of the potential risk factors examined achieved statistical significance, but maternal night blindness increased the risk of colonization 3-fold. The odds of carrying a PncCRM197 vaccine serotype were increased among infants born to mothers who experienced night blindness during pregnancy. The most prevalent serogroups/types during the first 6 months of life were 6, 9, 10, 11, 14, 15, 19, 23 and 33, accounting for 76.7% of all serotyped isolates.South Indian infants experience high rates of pneumococcal carriage during the first 6 months of life, which may partially explain their increased risk for pneumonia.