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Abstract Background Minisatellites and microsatellites are associated with human disease, not only as markers of risk but also involved directly in disease pathogenesis. They may play significant roles in replication, repair and mutation of DNA, regulation of gene transcription and protein structure alteration. Phenotypes can thus be affected by mini/microsatellites in a manner proportional to the length of the allele. Here we propose a new method to assess the linear trend toward transmission of shorter or longer alleles from heterozygote parents to affected child. Results This test (trend-TDT) performs better than other TDT (Transmission/Disequilibrium Test) type tests, such as TDTmax and TDTL/S, under most marker-disease association models. Conclusion The trend-TDT test is a more powerful association test when there is a biological basis to suspect a relationship between allele length and disease risk.