Objective The aim of this study was to determine the colonization rate of Streptococcus pneumoniae , antimicrobial susceptibility pattern and associated risk factors among children attending kindergarten school in Hawassa, Ethiopia. Results Out of 317 study participants, 68 (21.5%) were colonized with S. pneumoniae . Colonization rate was significantly associated with factors such as age (3 to 4 years old) (P = 0.01), having a sibling whose age was less than 5 years (P = 0.011), sharing a bed with parents (P = 0.005), cooking within bedroom (P = 0.002), and previous hospitalization (P = 0.004). Forty-four (64.6%), 33 (48.5%), and 2942.6%) of S. pneumoniae isolated were resistant to cotrimoxazole, penicillin, and tetracycline respectively.