The stable conformations of both the trans- and cis-1,3-disubstituted Nb-benzyl stereoisomers of the Pictet - Spengler reaction have been determined by NMR spectroscopy and X-ray crystallography in order to better understand the C(1) -N(2) cis- to trans-isomerization process. In the Na-H series, the chair conformation was preferred for the trans-isomer 3a, while the cis-isomer 3b existed predominantly in the boat form. However, in the Na-methyl series (1a, 1b, 2a, 2b), both the cis (1b, 2b) and trans (1a, 2a) diastereomers existed in the chair conformation to relieve the A(1,2)-strain between the Na-methyl function and the substituent at C(1). The difference in the preferred conformations of the cis-isomers in the Na-H and Na-methyl series (as compared to the preferred conformations in the trans-isomers) can be employed to understand the reduced rate of epimerization of cis-2b into trans-2a as compared to 3b into 3a. This provides the structural basis for the carbocation-mediated intermediate in the C(1) - N(2) scission process.