Commercially available plasmid preparation kits are used in many laboratories to isolate plasmid DNA for subsequent dideoxy sequencing. We tested kits from seven different manufacturers for the purity of obtained plasmid preparations and compared the quality of sequencing results. The amount of RNA carry-over differed significantly (80–323 ng) and the usage of two kits led to protein remainders. Sequence read lengths (0–812 bases) and percentages of reading errors (1.6–100%) were also significantly different. We found the amount of protein contaminants to correlate with the percentage of reading errors (r = 0.63, P = 0.02).