The goal of this study was to determine whether frontal sinus hypoplasia coexists with maxillary sinus hypoplasia. Analyzing paranasal CT scans retrospectively, we included 86 patients who had a hypoplastic maxillary sinus at least on one side and 80 patients with bilateral normal maxillary sinuses (control group). We classified hypoplastic maxillary sinuses using the classification system previously defined by Bolger et al. (Otolaryngol Head Neck Surg 103(5):759-765, 1990). We classified the frontal sinuses as aplastic, hypoplastic, medium-sized, and hyperplastic; as previously defined by Guerram et al. (Am J Phys Anthropol 154(4):621-627, 2014). We compared the presence of frontal sinus hypoplasia using Chi-square test between the groups. The mean age of the maxillary sinus group was 43.2 (range 18-84) years. Of 86 patients, 33 (38.4%) had unilateral and 53 (61.6%) had bilateral maxillary sinus hypoplasia. Of 139 maxillary sinuses totally included, 73 (52.5%) were type 1, 51 (36.7%) were type 2 and 15 (10.8%) were type 3 hypoplastic maxillary sinuses. Of 332 frontal sinuses totally included, 25 (7.5%) were aplastic, 32 (9.6%) were hypoplastic, 172 (51.9%) were medium-sized, and 103 (31%) were hyperplastic. Of 86 patients with a hypoplastic maxillary sinus at least on one side, 29 (33.7%) had a hypoplastic and/or aplastic frontal sinus, while 10 (12.5%) had a hypoplastic and/or aplastic frontal sinus at least on one side in control group. Incidence of frontal sinus hypoplasia and/or aplasia was significantly higher in patients with maxillary sinus hypoplasia compared to the patients with bilaterally normal maxillary sinuses (χ = 10.384, P = 0.001). Maxillary sinus hypoplasia has a significantly higher coexistence with frontal sinus hypoplasia. This study may have an implication for anatomical studies about the development of the paranasal sinuses and paranasal sinus surgery as well as further morphological studies.