The anatomy of the pterygopalatine fossa keeps a traditional level and is viewed as constant, even though a series of structures neighboring the fossa are known to present individual variations. We aimed to evaluate on 3D volume renderizations the anatomical variables of the pterygopalatine fossa, as related to the variable pneumatization patterns of the bones surrounding the fossa. The study was performed retrospectively on cone beam computed tomography (CBCT) scans of 100 patients. The pterygopalatine fossa was divided into an upper (orbital) and a lower (pterygomaxillary) floor; the medial compartment of the orbital floor lodges the pterygopalatine ganglion. The pneumatization patterns of the pterygopalatine fossa orbital floor walls were variable: (a) the posterior wall pneumatization pattern was determined in 89.5 % by recesses of the sphenoidal sinus related to the maxillary nerve and pterygoid canals; (b) the upper continuation of the pterygopalatine fossa with the orbital apex was narrowed in 79.5 % by ethmoid air cells and/or a maxillary recess of the sphenoidal sinus; (c) according to its pneumatization pattern, the anterior wall of the pterygopalatine fossa was a maxillary (40.5 %), maxillo-ethmoidal (46.5 %), or maxillo-sphenoidal (13 %) wall. The logistic regression models showed that the maxillo-ethmoidal type of pterygopalatine fossa anterior wall was significantly associated with a sphenoidal sinus only expanded above the pterygoid canal and a spheno-ethmoidal upper wall. The pterygopalatine fossa viewed as an intersinus space is related to variable pneumatization patterns which can be accurately identified by CBCT and 3DVR studies, for anatomic and preoperatory purposes.