This article reports long-term infection and treatment failure in 18 symptomatic individuals infected with Blastocystis spp. Patients were initially treated with either metronidazole, iodoquinol or triple combination therapy consisting of nitazoxanide, furazolidone and secnidazole. Following treatment, resolution of clinical symptoms did not occur and follow-up testing revealed ongoing infection with the same subtype. Patients then underwent secondary treatment with a variety of antimicrobial agents but remained symptomatic with Blastocystis spp. still present in faeces. Sequencing of the SSU rDNA was completed on all isolates and four subtypes were identified in this group: ST1, ST3, ST4 and ST5. This study highlights the lack of efficacy of several commonly used antimicrobial regimens in the treatment of Blastocystis and the chronic nature of some infections. It also demonstrates the need for further research into treatment options for Blastocystis infection.