Onychomycosis is a common fungal nail infection that responds poorly to antifungals. To investigate the efficacy and safety of methyl aminolevulinate (MAL) photodynamic therapy (PDT) in the treatment of onychomycosis. A multicentre (3), randomized, placebo-controlled clinical trial compared the effects of three sessions of urea (40%) plus conventional MAL-PDT with urea (40%) plus placebo (red light) photodynamic therapy (pPDT) in onychomycosis patients. Efficacy, both clinical (onychomycosis severity index, OSI) and microbiological, was blindly evaluated after 36 weeks of follow-up. Forty patients were analysed in the trial. Twenty-two received MAL-PDT and 18 pPDT. A complete response (OSI = 0) was observed for four patients (18.18%) in the MAL-PDT group and one (5.56%) in the pPDT group (NTT 7.92, 95% CI: 2.98-9.69, P = 0.23). A decrease in OSI score of over 75% (OSI75) was achieved by 40.91% of the patients in the MAL-PDT group and 16.67% in the pPDT group (P = 0.096). Microbiological cure was achieved by seven patients (31.82%) in the MAL-PDT group and two (11.11%) in the pPDT group (P = 0.178). MAL-PDT resulted in better rates of clinical response [OSI >75%: 53.85% vs. 18.75% (P =0.048)] and microbiological cure [41.56% vs. 7.14% (P = 0.037)] in non-dystrophic vs. dystrophic onychomycosis patients. No significant side-effects were reported. The limitations of the study were the reduced sample size and the unexpected efficacy of the control treatment, which was attributed to the 40% urea pre-treatment. This study did not show significant differences between urea 40% + MAL-PDT and urea 40% + pPDT in the treatment of onychomycosis. However, some results suggest that this treatment may constitute an alternative for dermatophyte and non-dermatophyte mould onychomycosis in patients not eligible for systemic treatment, particularly in the absence of total nail dystrophy.