Extraction of large numbers of living and debris-free nematodes is based on the active downward migration of nematodes through muddy sediments. This study is an assessment of how representative the extracted nematode population is in comparison to the in situ population. Nematode extraction efficiencies ranged from 20-29%; however, the method yielded 153 000 and 223 000 debris-free nematodes in 48 h (per m2 of mud with nematode population density of 776 000 individuals m–2). Sieve mesh size, migration device mesh size, and size distribution and behaviour of nematode species all influenced the extraction results. The species composition of the extracted nematode populations was significantly different from the in situ population assemblage. Metachromadora remanei and M. vivipara migrated less efficiently than Ptycholaimellus jacobi, Chromadora macrolaima and Daptonema oxycerca. This bias should be monitored in experimental studies using nematode populations extracted by means of sieving and downward migration.