To estimate the burden of complex perianal fistulae (CPF) in adult patients with Crohn’s disease (CD) in Portugal mainland during 2017, using disability adjusted life years (DALY). The burden of disease follows a prevalence based approach. It was assumed that no deaths were due specifically to CPF in CD. Therefore only years lost due to disability (YLD) were estimated using a methodology in stages. First, a pharmacoepidemiological approach was used to estimate the prevalence of inflammatory bowel disease patients treated with biological agents, based on the latest national sales data. Second, the proportions of these with CD and, in this group, of those receiving anti-tumour necrosis factor treatment were used to estimate prevalent patients with CD. Finally, prevalence rates of CPF in CD were based on the literature. Next a cumulative incidence model of CPF in CD patients was used to estimate the prevalence in each disease state: active fistulae; fistulae closure; post successful surgery; post unsuccessful surgery. Disability weights per health state were based on utility values from cost-utility studies. In 2017, 3.080 CD patients had been previously diagnosed with CPF and 741 had an active CPF. With DALY solely based on YLD, the overall burden for 2017 was estimated at 996 DALY, of which 382 DALY were due to the active phase of the disease. The average burden per patient was estimated at 0.08 DALY per CD patient and at 0.52 DALY per patient with an active CPF in CD. In 2017, CPF-CD was responsible for a burden of 996 DALY, of which 382 are due to the active phase of the disease. Despite the low prevalence of CPF in CD, the burden of disease per patient is high. This reflects the importance of the disease and justifies further attention from healthcare decision makers.