The present invention provides methods, kits and compositions for high fidelity nucleic acid amplification reactions of target nucleic acids such that specific amplification products that incorporate non-standard bases are produced. The amplification reactions can either be linear or exponential. In some embodiments, the fidelity of the amplification reaction is high enough such that a majority of the amplification products maintain non-standard bases at specific sites designated by the user after a specified number of amplification cycles. In some embodiments, the ratio of non-standard nucleoside triphosphates is greater than the amount of standard nucleoside triphosphates initially present in the reaction mixture.