The duplicate method for estimating uncertainty from measurement including sampling is presented in the Eurachem/CITAC guide. The applicability of this method as a tool for verifying sampling plans for mycotoxins was assessed in three case studies with aflatoxin B(1) in animal feedingstuffs. Aspects considered included strategies for obtaining samples from contaminated lots, assumptions about distributions, approaches for statistical analysis, log(10)-transformation of test data and applicability of uncertainty estimates. The results showed that when duplicate aggregate samples are formed by interpenetrating sampling, repeated measurements from a lot can be assumed to approximately follow a normal or lognormal distribution. Due to the large variation in toxin concentration between sampling targets and sometimes very large uncertainty arising from sampling and sample preparation (U(rel) ≥ 50%), estimation of uncertainty from log(10)-transformed data was found to be a more generally applicable approach than application of robust ANOVA.