A new method of sample preparation was developed for MALDI-TOF-MS analysis of oligonucleotides. First, aqueous DNA samples are dispensed and allowed to dry. Then 6-aza-2-thiothymine matrix dissolved in nonaqueous volatile solvents is applied on top of the DNA residue to form a thin homogeneous film. MALDI-TOF analysis shows such preparation generates much better shot-to-shot and sample-to-sample reproducibility and essentially eliminates the need to search for "hot" spots. The increased homogeneity of the matrix/analyte crystal distribution results in significant improvement for quantitative and high-throughput analyses of DNA. Using this method, isotopically resolved oligonucleotide spectra up to a 24-mer can also be easily obtained in a reflectron instrument. Due to the ease of preparation, this method could be widely useful for a number of applications such as for assays that are performed on surface in vitro, as the thin-layer matrix could be applied directly for MALDI analysis.