Background: Current studies have demonstrated the efficacy and safety of laser intervention in the treatment of onychomycosis. The objective of this study was to compare the efficacy of long-pulsed Nd:YAG 1064 nm laser for treatment of toenails onychomycosis with fingernails onychomycosis. Methods: One hundred and twelve affected fingernails or toenails in 37 patients with onychomycosis were randomized into Group 1 (22 patients with 50 affected fingernails) and Group 2 (15 patients with 62 affected toenails). These patients were further classified into three subgroups (Grade II, III, and IV) according to Scoring Clinical Index of Onychomycosis. All the affected nails were treated with long-pulse Nd:YAG 1064 nm laser intervention, once weekly, for continuous weeks, and were followed up for 24 weeks. Results: The response rates at weeks 8, 16, and 24 were 0, 0 and 52%, respectively, for Group 1, and 10, 32 and 71% for Group 2. The inter-group difference in efficacy was statistically significant (P<0.05). Even in the same subgroup, the response rate of Group 2 was higher than that of Group 1. Conclusions: The efficacy of long-pulsed Nd:YAG 1064 nm laser intervention against affected toenails is superior to that against fingernails. It is also effective for treatment of onychomycosis with different severity.