The 7-valent pneumococcal conjugate vaccine became available in Portugal in 2001. Although not included in the national immunization program, vaccination coverage is high (over 60%). We studied for the first time the rates of nasopharyngeal (NP) carriage of pneumococci, antibiotic resistance patterns and serotypes among children attending day-care centers (DCCs) in Coimbra, a city in the Central Region of Portugal. Between January and February 2007, a cross-sectional study was conducted among children aged 6 months to 6 years attending eight DCCs. NP swabs were obtained from 507 children: 76.7% had received at least one dose of 7-valent pneumococcal conjugate vaccine and 64.3% were age-appropriately vaccinated. The global pneumococcal carriage rate was 61.3%. Colonization proportions varied with age and number of children attending each DCC. Serotyping revealed that 20.7% of the pneumococci were vaccine types (VTs), 70.8% were non-VTs, and 8.5% were nontypeable. Serotype 19F was the second most frequent serotype being detected in 10.5% of the samples. While global NP carriage was not associated with vaccination status, non-VTs were predominant among vaccinated children, who had significantly lower prevalence of VT. Of all isolates, 15.7% had penicillin minimum inhibitory concentrations that ranged between 0.12 and 2 mu g/ml. The proportion of resistant strains was significantly higher among VT and unvaccinated children. In conclusion, the rates of vaccination and prevalence of pneumococcal NP were high. Rates of antimicrobial resistance were similar to those found in studies conducted in Oeiras and Lisbon. This study is a platform for future surveillance activities.