Background Recent research shows that lasers can inhibit fungal growth and that Nd:YAG 1064-nm lasers can penetrate as deep as the lower nail plate. The aim of this study was to observe the effect of a long-pulse Nd:YAG 1064-nm laser on 154 nails of 33 patients with clinically and mycologically proven onychomycosis. Methods Thirty-three patients with 154 nails affected by onychomycosis were randomly assigned to two groups, with the 154 nails divided into three sub-groups (II degree, III degree, and IV degree) according to the Scoring Clinical Index of Onychomycosis. The 15 patients (78 nails) in group 1 were given eight sessions with a one-week interval, and the 18 patients (76 nails) in group 2 were given four sessions with a one-week interval. Results In group 1, the effective rates at 8 weeks, 16 weeks, and 24 weeks were 63%, 62%, and 51%, respectively, and the effective rates in group 2 were 68%, 67%, and 53% respectively. The treatment effect was not significantly different between any sub-group pair (P >0.05). Conclusions Long pulse Nd:YAG 1064-nm laser was effective for onychomycosis. It is a simple and effective method without significant complications or side effects and is expected to become an alternative or replacement therapy for onychomycosis. Chin Med J 2012;125(18):3288-3291