We evaluated nasopharyngeal colonization with erythromycin-resistant Streptococcus pneumoniae during the first 2 years of life in central and southern Greece. Of 2448 children studied from February 1997 to February 1999, 766 (31%) carried 781 pneumococcal isolates. Ninety-five (3.9%) of the children attended day care centers. Eighteen percent of the pneumococci were resistant to erythromycin (minimal inhibitory concentration 1 to >128 microg/mL), with 67.9% of them carrying the erm(B) gene and 29.2% mef(A) gene products. Four strains possessed neither the erm(B) nor the mef(A) gene. Multidrug resistance occurred in 97% and 40% of isolates carrying the erm(B) and mef(A) gene, respectively. An association was found between the erm(B) gene and serotypes 6B and 23F and between the mef(A) gene and serotypes 14 and 19F. A significant relationship existed between carriage of erythromycin-resistant pneumococci and use of macrolides or beta-lactams in the previous 3 months; the association was strongest when macrolide therapy was administered during the last month (odds ratio, 5.92; P=.0001). The findings indicate the necessity of a judicious use of both macrolides and beta-lactams in young children to reduce the colonization with erythromycin-resistant pneumococci and the subsequent spread of such strains to the community.