Objective. This study describes geometry-based and intensity-based tools for quality assurance (QA) of automatically generated structures for online adaptive radiotherapy, and designs an operator-independent traffic light system that identifies erroneous structure sets. Approach. A cohort of eight head and neck (HN) patients with daily CBCTs was selected for test development. Radiotherapy contours were propagated from planning computed tomography (CT) to daily cone beam CT (CBCT) using deformable image registration. These propagated structures were visually verified for acceptability. For each CBCT, several error scenarios were used to generate what were judged unacceptable structures. Ten additional HN patients with daily CBCTs and different error scenarios were selected for validation. A suite of tests based on image intensity, intensity gradient, and structure geometry was developed using acceptable and unacceptable HN planning structures. Combinations of one test applied to one structure, referred to as structure-test combinations, were selected for inclusion in the QA system based on their discriminatory power. A traffic light system was used to aggregate the structure-test combinations, and the system was evaluated on all fractions of the ten validation HN patients. Results. The QA system distinguished between acceptable and unacceptable fractions with high accuracy, labeling 294/324 acceptable fractions as green or yellow and 19/20 unacceptable fractions as yellow or red. Significance. This study demonstrates a system to supplement manual review of radiotherapy planning structures. Automated QA is performed by aggregating results from multiple intensity- and geometry-based tests.