Abstract: The incidence of Streptococcus pneumoniae isolated from pediatrics admitted into various hospitals in Ekiti and Ondo States from the months of January 2009 to July 2010 were investigated. It was observed that out of the 400 samples collected from children in both states, 57 (14%) were positive for the isolates, while 295 (74%) were negative. Indicating a low incidence in both states but higher in Ondo State. Out of the 57 positive samples, 44 (77%) were isolates from sputum, 4 (7%) from urine, 1 (2%) from blood and 8 (14%) from ear swab. The highest number of positive isolates were 41 (68%) from males while 16(32%) were from females. From sputum, 33 (97%) were susceptible to Ciprofloxacin and 5(14%) to Cloxacillin. From urine, 3(75%) isolates were susceptible to Ofloxacin. The isolates from blood samples were susceptible to both Ciprofloxacin and Gentamycin. The isolates from ear swab were susceptible to Erythromycin and Ciprofloxacin but 1(50%) was susceptible to Ofloxacin, Clindamycin, Gentamycin, Cotrimoxazole Ampicilin and Cloxacillin. All isolates from urine samples show resistance to majority of the antibiotics. All isolates from blood showed resistance to all antibiotics tested except Ciprofloxacin and Gentamycin. Two isolates from ear swab showed resistance to Ceftriaxone and Argumentin. The most active antibiotics tested were Ciprofloxacin (92%), Gentamycin (78%), Erythromycin (70%), Ofloxacin (60%) and Clindamycin (46%).