Between 1997 and 2000 nasopharyngeal specimens were obtained from 466 children < or = 12 years old attending the Pediatric Emergency Department at S. Francisco Xavier Hospital, Lisbon, to evaluate risk factors for nasopharyngeal carriage of Haemophilus influenzae and Streptococcus pneumoniae and to characterize their phenotype and antimicrobial susceptibility. The attending pediatrician completed written questionnaires about the children's demographic and clinical histories. Over half the children (52.8%) carried H. influenzae and/or S. pneumoniae. Forty-one percent of these children had H. influenzae, 22.8% had S. pneumoniae and 36.2% had both. Risk factors identified for carriage of respiratory pathogens were: age below 3 years (p < 0.05), black race (p < 0.01), attending a daycare center (p < 0.05), and having a lower respiratory infection (p < 0.05). Asthmatic children were less likely to be carriers (p = 0.004). About two-thirds of H. influenzae isolates were susceptible to all antibiotics tested, 7.9% were beta-lactamase producers, 16.4% were nonsusceptible to trimethoprim, and 6.9% were intermediately resistant to clarithromycin. Over half (57.1%) of S. pneumoniae isolates were susceptible to all antibiotics tested, 21.1% were multiresistant, 23.3% were nonsusceptible to penicillin, and about 20% were resistant to macrolides. Low-level resistance to third-generation cephalosporins was detected in 2.3%. The data reflect the controversy surrounding risk factors of nasopharyngeal colonization. These may have significant implications on clinical practice and on antimicrobial strategies to prevent the appearance of further resistant strains. Our findings highlight the importance to investigate the relationship between asthma and carriage.