An algorithm is presented for the efficient semi-automatic construction of a detailed reference standard for registration in thoracic CT. A well-distributed set of 100 landmarks is detected fully automatically in one scan of a pair to be registered. Using a custom-designed interface, observers locate corresponding anatomic locations in the second scan. The manual annotations are used to learn the relationship between the scans and after approximately twenty manual marks the remaining points are matched automatically. Inter-observer differences demonstrate the accuracy of the matching and the applicability of the reference standard is demonstrated on two different sets of registration results over 19 CT scan pairs.