The purpose of this study was to evaluate the hypothesis that the nasopharyngeal anatomy has influence in the risk of recurrent acute otitis media (AOM) attacks. We analysed the occurrence of acute otitis media in 238 healthy schoolchildren who were X-rayed for orthodontic purposes. Six measurements reflecting the size and shape of the bony nasopharynx were recorded from lateral cephalograms. The means for almost all the dimensions of the bony nasopharynx measured were smaller in the children with two or more attacks of AOM in their history than in those with no attack or only one attack. Logistic multivariate modelling showed the distance from the posterior nasal spine to the sella-basion line to be a significant risk factor for recurrent otitis media in girls (difference 1.0 mm; 95 per cent confidence interval 0.1–2.0 mm; p = 0.04) and the shape of the nasopharynx (roundness) in boys (difference 1.9 mm; 95 per cent confidence interval 0.1–4.0 mm; p = 0.01). Measuring the nasopharyngeal bony dimensions may help to identify those children with a risk of recurrent otitis media, at whom prophylactic therapies should be targeted.