Background: There is little evidence in the management of refractory giardiasis after treatment with nitroimidazoles. This study estimates the proportion of persistent giardiasis in 3 hospitals in Barcelona, describes risk factors and genotype associated and evaluates the efficacy rate of quinacrine in those with persistent giardiasis. METHODS: A clinical prospective observational study was conducted in patients with giardiasis treated with nitroimidazoles. Those with persistent giardiasis were provided quinacrine. Molecular characterization of Giardia isolates was performed by PCR amplification of a fragment of tpi and bg genes. RESULTS: Seventy-seven patients were recruited and treated with nitroimidazoles and in 14/71 of patients followed-up(20%), Giardia persisted. Refractory giardiasis was associated with malaise(p:0.007) and anorexia(p:0.019), with previous giardiasis(p:0.034) and with previous antibiotic(p:0.02) or antiparasitic(p:0.037). Quinacrine had an effectiveness rate of 100% in refractory giardiasis(n=13,95%CI 75-100). Molecular characterization showed that 17(25%) Giardia isolates belonged to assemblage A, 31(43%) to assemblage B. In refractory giardiasis, assemblage B and A were found as responsible in 6 and 4 cases respectively. CONCLUSIONS: Almost 20% of patients presented persistent giardiasis after nitroimidazole being both assemblage A and B involved. Short course of quinacrine was effective in treating refractory cases and further controlled studies should evaluate its efficacy and safety.