The presence of the Onodi cell (OC) may be accompanied by morphological variations of the neighboring anatomic structures. Such variations carry significant surgical implications and challenges. Pneumatization of the sphenoid sinus induces anterior clinoid pneumatization (ACP), affects the type of the Vidian nerve (VN) canal or alters the courses of the internal carotid artery (ICA), and the optic nerves (ONs) are strongly depending on it. Onodi cell pneumatization may reach and surround the optic nerve in various extension. Our aim in the study was to investigate the effect of Onodi cell's potential co-existence on these structures. This study was planned as a retrospective and cross-sectional study. This study performed in a tertiary referral center. Coronal computerized tomography images of 999 patients were examined. Using an 64 slices tomography machine, images taken at 3-mm sections were reconstructed using a bone algorithm and evaluated. OCs were present at 212 of the total 320 sides in 160 patients. Type-2 was found to be the most prevalent type of VN canal configuration (Type-2: VN canal partially protrudes into the sphenoid sinus or into the floor of the sphenoid) among all patients (66.5 %) and among those with OCs (71.2 %). The presence or absence of the OC did not cause a statistically significant alteration of the intrasphenoidal course of the VN. The presence of OCs was found to be significant (p < 0.01) in accompanying pneumatization of the anterior clinoid process (34.4 %, 73/212), protrusion (80.1 %, 170/212) and dehiscence (36.3 %, 77/212) of the optic nerve, and protrusion (59 %, 125/212) and dehiscence (20.8 %, 44/212) of the ICA. In 108/320 sides where OCs were absent, no significant correlations existed. This study shows that in the co-existence of an OC, ACP, protrusion and dehiscence of the optic nerve and ICA are encountered at significantly higher rates, while the course of the VN is not necessarily altered.