The primary aldosteronism (PA) subtype is usually confirmed by CT and adrenal venous sampling (AVS). However, the subtype diagnosis by AVS is not necessarily consistent with the subtype diagnosis by CT. Patients with PA who show bilateral lesions (normal-appearing adrenals or bilateral adrenal nodules) on CT but unilateral disease on AVS are often found. The aim of this study was to evaluate whether patients with PA subtype discordance between CT and AVS obtain benefits from unilateral adrenalectomy. We retrospectively analyzed 362 consecutive patients with PA who underwent both CT and adrenocorticotropic hormone-unstimulated AVS at Kanazawa University Hospital. Surgical outcomes for unilateral PA were evaluated according to the criteria of the Primary Aldosteronism Surgical Outcome study. In our study, the success rate of AVS in patients with bilateral lesions on CT was 89% (191/214). Furthermore, the discordance rate between CT and AVS in patients with bilateral lesions on CT was 39% (74/191). After surgery, patients with bilateral lesions on CT but unilateral disease on AVS (n = 17) had a lower complete biochemical success rate than those with unilateral lesions on CT and ipsilateral disease on AVS (n = 30) (41% vs. 80%, p = 0.01), but clinical and biochemical benefits (the complete and partial success combined) were not significantly different between them (76% vs. 93% (p = 0.11) and 70% vs. 90% (p = 0.10), respectively). In conclusion, patients with bilateral lesions on CT but unilateral disease on AVS benefited from surgery, and AVS should be performed for patients who pursue surgical management when the CT findings suggest bilateral lesions.