Antimicrobial resistance of pneumococci is influenced by serotypes, antimicrobial consumption and vaccine use. Serotyping of 697 out of 1331 pneumococcal isolates, recovered in Portugal from 1994 to 2004, showed that the theoretical rate of heptavalent conjugate vaccine coverage was 91.7% and 63.6% for penicillin and erythromycin non-susceptible strains, respectively, in children up to 1 year old. The use of amoxicillin and erythromycin decreased in the vaccine period 2001-2004 (P=0.04 and P<0.01, respectively) but azithromycin usage increased in the same period (P<0.01). By using linear regression models, we evaluated the role of antimicrobial and vaccine use in the trends of resistance to penicillin and erythromycin among the isolates. The models suggest that the use of macrolides was the main factor associated with an increase of penicillin and erythromycin non-susceptible isolates from adults (P<0.01) and erythromycin non-susceptible isolates among children (P=0.006). These models also suggest that heptavalent vaccine is failing to reduce antimicrobial resistance as expected, possibly due to the increased consumption of azithromycin (P=0.04). The efficient use of new antibiotics may reverse the present trends of antimicrobial resistance.