To assess the anatomical background and significance of incomplete invasive coronary angiography (ICA) and to evaluate the value of coronary computed tomography angiography (CTA) in this scenario. The current study is an analysis of high volume center experience with prospective registry of coronary CTA and ICA. The target population was identified through a review of the electronic database. We included consecutive patients referred for coronary CTA after ICA, which did not visualize at least one native coronary artery or by-pass graft. Between January 2009 and April 2013, 13,603 diagnostic ICA were performed. There were 45 (0.3 %) patients referred for coronary CTA after incomplete ICA. Patients were divided into 3 groups: angina symptoms without previous coronary artery by-pass grafting (CABG) (n = 11,212), angina symptoms with previous CABG (n = 986), and patients prior to valvular surgery (n = 925). ICA did not identify by-pass grafts in 21 (2.2 %) patients and in 24 (0.2 %) cases of native arteries. The explanations for an incomplete ICA included: 11 ostium anomalies, 2 left main spasms, 5 access site problems, 5 ascending aorta aneurysms, and 2 tortuous take-off of a subclavian artery. However, in 20 (44 %) patients no specific reason for the incomplete ICA was identified. After coronary CTA revascularization was performed in 11 (24 %) patients: 6 successful repeat ICA and percutaneous intervention and 5 CABG. Incomplete ICA constitutes rare, but a significant clinical problem. Coronary CTA provides adequate clinical information in these patients.