Primers currently used for amplification of locus DYS385 on the Y chromosome give quite long amplicons that are difficult to resolve on native polyacrylamide gels. We therefore designed new primers that give much shorter products for easy separation. With this system, two allele variants that were characterized by sequencing as 14.1 (GAAA --> GAAAA) and 14.2 (GA insertion), were identified in two unrelated Northern Thai men due to their decreased mobility. Interestingly, initial capillary electrophoresis mistyped the 14.1 variant amplified with the traditional primers as allele 14. Forty different haplotypes were found in 147 Northern Thais with a haplotype diversity of 0.9430. Haplotype 13-18 (frequency 0.136) is the most frequent one: for comparison: haplotype 14-18 (frequency 0.074) was found to be the most common in a population from Bangkok (n = 95) in an earlier study. This striking difference within Thailand's population probably results from genetic differences in the founding populations.