Keypoints Positive pathogen colonisation in 70% of (AOM) patients with acute otitis media, including Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis after standard antibiotic therapy could be associated with a high possibility of AOM recurrence. High frequency of penicillin non-susceptible S. pneumoniae isolates in children with recalcitrant AOM was observed. During post-treatment control visits, penicillin non-susceptible strains constituted 100% of isolated pneumococci. Prevalence of β-lactamase-positive H. influenzae strains increased to 64.7% of isolates comparing to 56% isolated in AOM. There was correspondence between the pathogen species isolated during AOM and during control visit after treatment in about 49% patients. S. pneumoniae-positive culture from nasopharyngeal samples may provide an accurate proxy for the positive MEF culture when MEF samples cannot be obtained. Older children, not attending day care institutions with shorter time of antibiotic therapy, were at risk of recalcitrant AOM. Moreover, risk of pathogen colonisation after treatment was associated with younger age, and bilateral ear infection in the studied children. Nasopharyngeal pneumococcal colonisation rates were significantly higher than oropharyngeal and contrary to H. influenzae colonisation which was found significantly higher in oropharyngeal samples.