Objective The conventional criteria for defining the basilar invagination (BI) focus on the relationship of odontoid tip to basion and opisthion, landmarks that are intrinsically variable especially in presence of occipitalised atlas. A universal single reference line is proposed that helps in unequivocally establishing the diagnosis of BI, may be relevant in establishing both Goel types A and B BI, as well as in differentiating a ‘very high’ from ‘regular’ BI. Methods Study design – case-control study. In 268 patients (group I with BI [n = 89] including Goel type A BI [n = 66], Goel type B BI [n = 23], and group II controls [n = 179]), the perpendicular distance between odontoid tip and line subtended between posterior tip of hard palate-internal occipital protuberance (P-IOP line) was measured. Logistic regression analysis determined factors influencing the proposed parameter (p < 0.05). Results In patients with a ‘very high’ BI (n = 5), the odontoid tip intersected/or was above the P-IOP line. In patients with a ‘regular’ BI (n = 84), the odontoid tip was 6.56 ± 3.9mm below the P-IOP line; while in controls, this distance was 12.53 ± 4.28 mm (p < 0.01). In Goel type A BI, the distance was 7.01 ± 3.78 mm and in type B BI, it was 5.07 ± 4.19 mm (p = 0.004). Receiver-operating characteristic curve analysis identified 9.0 mm (8.92–9.15 mm) as the cut-point for diagnosing BI using the odontoid tip-P-IOP line distance as reference. Conclusion The odontoid tip either intersecting the P-IOP line (very high BI) or being < 9 mm below the P-IOP line (Goel types A and B BI) is recommended as highly applicable criteria to establish the diagnosis of BI. This parameter may be useful in establishing the diagnosis in all varieties of BI.