This study was carried out to examine the incidence, morphology and clinical implication of antral septa. Out of 265 maxillary sinuses, 65 sinuses in atrophic maxillae were examined clinically during sinus floor elevation and 200 sinuses examined radiographically (CT), the latter being further subdivided into non-atrophic/dentate and atrophic/edentulous maxillary segments. Eighteen (27.7%) out of 65 clinically-examined maxillae and 32 (16%) out of the 200 non-preselected CT-examined maxillary sinuses showed antral septa. CT-topogram subclassification revealed 21 septa (13.2%) in 159 non-atrophic and 11 septa (26.8%) in 41 atrophic maxillary segments (P < 0.01). Morphologically, CT examination yielded one complete septum (0.5%), 21 incomplete septa on the sinus floor and 10 incomplete septa on the anterior antral wall (5%). CT revealed a significantly greater dimension of antral septa in non-atrophic maxillary segments than in atrophic ones (P < 0.01). In atrophic maxillary sinuses, the incidence (27.7% vs 26.8%), morphology (all septa located on sinus floor) and height (8.1 +/- 2.5 mm vs 6.8 +/- 1.6 mm) did not differ between the clinical and the CT examinations. Detailed knowledge about location, morphology and height of antral septa is clinically relevant to reduce the rate of complications when maxillary sinus surgery, i.e. sinus floor elevation, is carried out.