To investigate the phenomenon that PCR of Leishmania (V.) lainsoni minicircles using primers B1 and B2 gives anomalous small-sized products, unlike all other members of the Leishmania Viannia subgenus, cloned kDNA minicircles from L. (Viannia) lainsoni were sequenced using fluorescent dye terminator reactions. The sequence of L. (V.) lainsoni where the primer B2 would be expected to bind, was different from the other members of the L. Viannia subgenus, matching in only 7 out of 19 bases with the sequence of L. (V.) braziliensis at this position. The sequence obtained from the cloned minicircles enabled the design of a new primer which, when combined with B1, allowed the amplification of full sized minicircles in L. (V.) lainsoni, but not other members of the L. Viannia subgenus. Comparison of the sequence obtained for Leishmania (V.) lainsoni with other Leishmania minicircle DNA confirms that Leishmania (V.) lainsoni is more similar to members of the L. Viannia subgenus than to other Leishmania, but is distinctly different.