Objective Computed tomography colonography (CTC) is an alternative diagnostic test to colonoscopy for colorectal cancer and polyps. The aim of this study was to determine test characteristics important to patients and to examine trade-offs in attributes that patients are willing to accept in the context of the diagnosis of colorectal cancer. Methods A discrete choice study was used to assess preferences of patients with clinical indications suspicious of colorectal cancer who experienced both CTC and colonoscopy as part of a diagnostic accuracy study in South Australia. Results were analyzed by using a mixed logit model and presented as odds ratios (ORs) for preferring CTC over colonoscopy. Results Colonoscopy was preferred over CTC as the need for a second procedure after CTC increased (OR of preferring CTC to colonoscopy = 0.013), as the likelihood of missing cancers or polyps increased (OR of preferring CTC to colonoscopy = 0.62), and as CTC test cost increased (OR of preferring CTC to colonoscopy = 0.650.80). CTC would be preferred to colonoscopy if a minimal bowel preparation was available (OR = 1.7). Some patients were prepared to trade off the diagnostic and therapeutic advantage of colonoscopy for a CTC study with a less intensive bowel preparation. Preferences also varied significantly with sociodemographic characteristics. Conclusions Despite CTC's often being perceived as a preferred test, this may not always be the case. Informed decision making for diagnostic tests for colorectal cancer should include discussion of the benefits, downsides, and uncertainties associated with alternative tests, as patients are willing and able to make trade-offs between what they perceive as the advantages and disadvantages of these diagnostic tests.