The secondary amide peptide bonds that comprise up to one-third of the bonds of peptide or protein backbones can exist as cis and trans isomers, with the trans isomer being highly favored. However, there is little quantitative data on the kinetics and equilibria of cis-trans isomerization of secondary amide peptide bonds due to the difficulty of detecting the very small Population of cis isomers. Knowledge of factors that influence the kinetics and equilibria of cis-trans isomerization of secondary amide peptide bonds will contribute to a more complete understanding of the structural and dynamic behavior of the backbones of peptides and unfolded proteins and of complex protein folding kinetics. We have characterized the kinetics and equilibria of cis-trans isomerization of the Xaa-Yaa secondary amide peptide bonds of the linear dithiol and cyclic disulfide forms of the peptides Ac-Cys-Xaa-Yaa-Cys-His-NH2, where Xaa-Yaa is Ala-Phe, Phe-Ala, Ala-Tyr, and Tyr-Ala, by H-1 NMR. Resolved resonances were observed for the Ala-methyl protons of the trans and the much less abundant cis isomers due to differential shielding of the Ala-methyl protons of the trans and cis isomers by ring current effects from the Phe and Tyr side chains. The Population of the cis isomers was determined from the relative intensities of the Ala-methyl resonances for the trans and cis isomers, and rate constants for cis-to-trans and trans-to-cis isomerization were determined by the magnetization transfer NMR method. The population of the cis isomers ranges from 0.07 to 0.12%, and the rate constants indicate that, when there is a trans-to-cis interchange, it is rapidly followed by a cis-to-trans interchange back to the more stable trans conformation. Although cyclization by disulfide bond formation imposes conformational constraints on the peptide backbones, cyclization is found to have relatively small affects on the dynamics of cis-trans isomerization.