Four kinds of aminosilane layers on glass slides or silicon wafers were prepared. The amine densities of the layers prepared with aminopropylmonoethoxydimethylsilane (APDES), aminopropylmonoethoxydimethylsilane (APMES), a mixture of (aminopropyl)triethoxysilane (APTES) and n-butyltrimethoxysilane (n-BTMS) (v/v = 1:10) are 4.0(+/-0.8), 1.0(+/-0.2), and 0.30(+/-0.6) amine/nm(2), respectively. A substrate with much higher amine density, that is, 40(+/-8) amines/nm(2) was also prepared by allowing aziridine to polymerize on the APDES-treated substrate. AFM revealed that APDES-, APMES-, and APTES/n-BTMS-treated surfaces were relatively flat; on the other hand, an aziridine-treated surface showed embossed morphology. The amine substrates were allowed to react with a heterobifunctional linker succinimidyl 4-maleimido butyrate (SMB), and subsequently pentadecadeoxynucleotides were microarrayed on the SMB-treated substrates. Characteristics of the DNA microarrays including the dynamic range, the mismatch discrimination efficiency, and so forth were examined. Noteworthily, DNA microarrays on the aziridine-polymerized substrate showed much higher fluorescence intensity. At the same time, DNA microarrays from these four substrates were able to discriminate internal- and terminal-mismatched pairs, but the fluorescence ratio was far from the one that thermodynamics implies.