Blastocystis is a common unicellular intestinal parasite in humans. Its clinical relevance is still subject to discussion with numerous conflicting reports on its ability to cause disease. A remarkable genetic heterogeneity among isolates suggests an association between distinct subtypes (STs) and pathogenicity, although a clear correlation between symptoms and subtype is lacking. Here, we report on a clinical case which possibly links Blastocystis sp. ST2 infection with the simultaneous occurrence of gastrointestinal illness and generalized chronic urticaria. Despite repeated chemotherapy with different antimicrobial drugs, both the gastrointestinal and cutaneous disorders reoccurred after short symptom-free intervals. Eradication of the parasite and permanent resolution of the patient's medical condition was finally achieved with the combined application of metronidazole and paromomycin.