Background: Nontypeable Haemophilus influenzae (NTHi) is one of the main respiratory pathogens associated with otitis media and lung infections in Australian Indigenous children. PHiD-CV10, the 10-valent pneumococcal conjugate vaccine containing H. influenzae protein D was used in the Northern Territory infant vaccination schedule for two years from October 2009. Methods: NTHi isolates from nasopharyngeal and ear discharge samples collected before, during and after the PHiD-CV10 era were screened for the hpd gene by PCR. Target amplicon sequence, extracted from available genomic sequence data, was analysed to identify variability in this region. Results: There was no statistically significant difference in the proportion of hpd#3-PCR negative isolates from each era; overall 7% and 6% of nasopharyngeal and ear discharge isolates were negative, respectively. The nucleotide sequence data supported the hpd-PCR findings; truncations of the hpd gene precluding amplification and presumably expression of protein D were observed in approximately 7% of available genomes. Conclusions: In the Northern Territory of Australia, a population at high risk of NTHi-associated infection, PHiD-CV10 use did not select for hpd-PCR negative isolates.