Hidradenitis suppurativa (HS) and pilonidal cysts are chronic, inflammatory skin conditions involving apocrine gland-bearing skin. Treatment is limited and unsatisfactory. Photodynamic therapy (PDT) has been reported to be safe and effective in the treatment of several off-label skin conditions. We report the case of a 29-year-old man affected by HS and pilonidal cysts since the age of 21. In the past, the patient was treated with antibiotics, corticosteroids and retinoids, without significant clinical improvement. Treatment with methyl aminolaevulinate (MAL)-PDT was started. A topical MAL cream (Metvix®) was applied to the affected areas with an occlusive dressing for 3 h and irradiated with a red light source. Therapy was repeated every 15 days for a total of nine applications. The patient completed a 6-month follow-up and achieved an almost complete clinical remission of the skin lesions (80%) and complete resolution of the itching and discomfort. This is the first case of HS associated with pilonidal cysts treated with MAL-PDT. MAL-PDT was effective and well tolerated in our patient. The costs of this therapy represent an important limitation, taking into account the high number of sessions that were performed compared with non-melanoma skin cancers.