We assessed risk factors affecting the provisional diagnosis of medically unexplained symptoms made by physicians in new patients, in 526 clinical encounters. Comparisons were made between the doctor's initial assessments regarding the nature of symptoms, and the final diagnosis. Physicians were more likely to err on the side of diagnosing the symptoms as medically explained rather than unexplained. When physicians perceived the interaction with the patient to be positive, they were more likely to make a provisional diagnosis that the symptoms were explained. Conversely, a negative perception of the interaction was associated with an increased likelihood of viewing symptoms as medically unexplained. Physicians should be aware of the effect of their own perceptions on their diagnostic behaviour.