Molecular techniques can be useful adjuncts to the diagnosis of onychomycoses. However, the nail presents difficulties in the extraction of its DNA. The comparison of three extraction protocols of DNA from nails and their ranking for possible use in the molecular diagnosis of onychomycoses are described. Extraction was performed on weighed nail clippings of equal size from positive (31) or negative (14) samples, according to the culture result. At Prot1, the extraction was performed according to Tahir and Watson, with an additional step implementing silica columns. At Prot2, the methodology proposed by the Statens Serum Institute of Copenhagen was used. At Prot3, DNA was extracted by the use of magnetic separation after homogenisation with glass beading. The evaluation parameters were DNA purity, DNA concentration, total DNA yield/g of tissue, cost and duration. The multiples of the means of medians of the first three parameters, for each protocol, were calculated. Prot3 showed the highest DNA purity. Prot2 presented the highest DNA concentration and DNA yield/g of tissue, while it was the cheapest and shortest. In total, the three protocols were graded as Prot2>Prot1>Prot3. The second method, although had a lower DNA purity, presented the higher DNA concentration and DNA yield, while its duration and cost were also favourable.