Introduction: Resistance to macrolide antibiotics is increasing in clinical isolates of Streptococcus pneumoniae and is associated with the presence of mobile genetic elements.Objetive: The aim of this study was to determine the distribution of serotypes and transposons among macrolide-resistant invasive isolates of S. pneumoniae in Colombia from 1994 to 2011.Materials and methods: A total of 225 macrolide-resistant S. pneumoniae isolates were analyzed. The isolates had epidemiological data, serotyping and antimicrobial susceptibility patterns. The phenotypes were tested by erythromycin-clindamycin double-disk test. We investigated the presence of transposons by several multiplex PCRs to identify the genes erm(B), mef(A), mef(E), tetM, Cat, Aph3-III, int-Tn916, xis-Tn916, TnpA-Tn917, TnpR-Tn917 and int-Tn5252.Results: Of all isolates, 62.7%, 2.7% and 34.6% of isolates exhibited cMLSB, iMLSB, and M phenotypes, respectively. Multiresistance was observed in 69.3% of these strains. The most prevalent genetic elements in MLSB were the Tn5253 (34%), mostly carried in serotype 6B isolates and found to be related to the international clone Spain-ST90; Tn1545 (18.4%), carried by serotype 19A and related to ST276, and Tn3872 (14.9%), mainly detected in capsular types 6B and 14. Other seven transposons (32.7%) were associated with different serotypes. The mega element (62.8%) was associated to serotype 6A and ST473 in M phenotype.Conclusions: The majority of erythromycin-resistance isolates of S. pneumoniae in Colombia had the cMLSB phenotype and was associated with the presence of transposons, which carry multiple resistance determinants for other antibiotics. Moreover, isolates with M phenotype carried the gene mef(E) in the mega element.