A comprehensive investigation of invasive Streptococcus pneumoniae was carried out in Brazil as part of the programme of the national epidemiological surveillance system. The investigation provided data on the trends of resistance to antimicrobial agents. A total of 6470 isolates of S. pneumoniae collected in the country from 1993 to 2004 were tested. During this period of time, the number of penicillin-resistant strains rose from 10·2 to 27·9 %. The proportions of intermediate and high-level resistant strains in 1993, which were 9·1 and 1·1 %, respectively, rose to 22·0 and 5·9 % in 2004. Geometric mean MICs for penicillin increased after the year 2000, to 0·19 μg ml−1 in 2004; most of these isolates were from patients with pneumonia and from children under 5 years old, and belonged to serotype 14. There was a significant increase in the number of isolates belonging to serotypes included in the 7-valent conjugate vaccine from children under 5 years old: from 48·6 % in 1993 to 69·6 % in 2004, mainly related to an increase in the frequency of serotype 14 isolates. From 2000 to 2004, meningitis isolates showed higher resistance rates to cefotaxime (2·6 %) compared to non-meningitis isolates (0·7 %); percentages of isolates resistant to trimethoprim-sulfamethoxazole, tetracycline, erythromycin, chloramphenicol and rifampicin were 65, 14·6, 6·2, 1·3 and 0·7 %, respectively. No levoflaxin resistance was observed. Multidrug resistance was identified in 4·6 % of isolates, of which 3·8 % were resistant to three classes, 0·7 % to four classes and 0·1 % to five classes of antimicrobial agent. The study provides valuable information that may support empirical antimicrobial therapy for severe S. pneumoniae infections in Brazil, and emphasizes the need for conjugate pneumococcal vaccination.