The script concordance test (SCT) is designed to assess clinical reasoning by adapting the likelihood of a case diagnosis, based on provided new information. In the standard instructions students are asked to exclude alternative diagnoses they have in mind when answering the questions, but it might be more authentic to include these. Fifty-nine final-year medical students completed an SCT. Twenty-nine were asked to take their differential diagnosis into account (adapted instructions). Thirty students were asked not to consider other diagnoses (standard instructions). All participants were asked to indicate for each question whether they were confused answering it with the given instructions (‘confusion indication’). Mean score of the test with the adapted instructions was 81.5 (SD 3.8) and of the test with the standard instructions 82.9 (SD 5.0) (p = 0.220). Cronbach’s alpha was 0.39 for the adapted instructions and 0.66 for the standard instructions. The mean number of confusion indications was 4.2 (SD 4.4) per student for the adapted instructions and 16.7 (SD 28.5) for the standard instructions (p = 0.139). Our attempt to improve SCTs reliability by modifying the instructions did not lead to a higher alpha; therefore we do not recommend this change in the instructional format.