Tuberous sclerosis complex (TSC) is a neurocutaneous disease with a high incidence of epilepsy and damaging effects on cognitive development. To understand the mechanisms leading to abnormal cognitive development, diffusion tensor imaging (DTI) techniques have begun to be used in recent years. The present study is the first to investigate differences in the microstructure and integrity of white matter tracts in adult patients with TSC and with and without epilepsy. A total of 37 patients with TSC (18 with epilepsy, median age 36 years; 19 without epilepsy, median age 35 years) without intellectual disability and autism spectrum disorder were included in the study. The control group (median age 34 years) comprised 37 individuals without psychiatric or neurodevelopmental disorders and neurological and cardiovascular diseases, diabetes, or addictions. A magnetic resonance imaging (MRI) DTI sequence was applied. There were differences in the average values of DTI parameters between patients with TSC and epilepsy and patients with TSC but without epilepsy in five white matter bands. When comparing the average values of DTI parameters between patients with TSC and epilepsy and healthy controls, we found differences in 15 of 20 analysed white matter fibres. White matter tracts in patients with TSC and epilepsy had more abnormalities than in patients with TSC but without epilepsy. The former group presented abnormalities in longer white matter fibres, especially in the left hemisphere. However, the latter group presented abnormalities in more medial and shorter white matter fibres. This DTI study documents the changes in the brain white matter of patients with TSC associated with the presence of epilepsy.