Background: Haemophilus influenzae is one of the main pathogens that cause community-acquired respiratory infections in children. Our previous study showed that Haemophilus influenzae is the second most common pathogen causing pneumonia and accounts for 30-50% of bacterial meningitis among Chinese children. Haemophilus influenzae carriage in children and its resistance to commonly used antimicrobials varies widely both geographically and over time. Results: Surveys of the nasopharyngeal carriage of Haemophilus influenzae in children younger than 5 years of age with acute respiratory tract infection (ARI) were conducted in Beijing Children's Hospital, China in 2000, 2002, 2010, and 2012. The overall annual carriage rates of Haemophilus influenzae among children younger than 5 years of age with ARI were 35.5%, 20.6%, 14.4%, and 18.7%, and the percentages of Haemophilus influenzae isolates producing beta-lactamase were 4%, 13%, 27.1%, and 31%, respectively. The percentages of susceptibility to ampicillin progressively decreased from 96% (2000) to 87% (2002) to 63% (2010) to 61% (2012). All of the ampicillin-resistant isolates were found to be beta-lactamase producers. The susceptibility to tetracycline increased from 54% (2000) to 60% (2002) to 91.5% (2010) to 94.5% (2012). No statistically significant differences were observed in the susceptibility to cefaclor, cefuroxime, sulfamethoxazole, and chloramphenicol. Amoxicillin/clavulanic acid and ceftriaxone were the most effective antimicrobials for the isolates of Haemophilus influenzae across the 10-year period. Conclusions: This report on the Haemophilus influenzae carriage rates in children and the susceptibility of these bacteria to commonly used antibiotics showed that Haemophilus influenzae carriage decreased from 2000 to 2012. Additionally, the percentage of beta-lactamase-producing isolates increased while their susceptibility to ampicillin progressively decreased during this time. These results indicate that the appropriate empirical antimicrobial therapy should be changed for pediatric patients in China.