We previously described a septal variant termed left atrial septal pouch (LASP). Present in a third of hearts, it results from incomplete fusion of the septum primum (SP) and septum secundum (SS). We assessed the prevalence of LASP using 64‐section multidetector computed tomography and further characterized the different variants. Among 864 scans, 770 were of sufficient quality for assessment (428 male, aged 59.2 ± 11.7 years). They were classified on the basis of the degrees of fusion of the SP and SS into a completely fused septum (CFS), patent foramen ovale (PFO), or LASP. The lengths of the SS, SP, and overlapping SP, the maximal length of the foramen ovale (FO) floor, and the atrial dimensions were compared. A PFO was seen in 181 patients (23.5%), a LASP in 242 (31.4%), and a CFS in 339 (44.0%). There were significant differences in the length of the SS (PFO—13.6 ± 4.3 mm, LASP—17.6 ± 4.8 mm, CFS—14.3 ± 7.7 mm, p < 0.001). Hearts with LASPs had a longer overlapping SP than those with PFOs (PFO—6.3 ± 4.5 mm, LASP—13.1 ± 5.2 mm, p < 0.001). The maximal lengths of the FO floor showed differences in short axis (SAX) view (PFO—21.7 ± 4.5 mm, LASP—15.3 ± 4.3 mm, CFS—16.3 ± 4.3 mm, p < 0.001). Hearts with PFO and LASP showed similar SP lengths (27.3 ± 6.6 mm vs. 26.4 ± 6.6 mm, p = 0.10). There was a positive linear correlation between the length of the SS and the overlapping SP (R2 = 0.28, p < 0.001) with a weaker negative correlation between the SS length and maximal length of the FO floor (R2 = 0.02, p < 0.001). The groups showed similar atrial dimensions and volumes. Present in a third of patients, hearts with LASP have longer SS and overlapping SP.