Acetylcarnitine, a naturally occurring compound found in high concentration in heart and skeletal muscle of vertebrates, bears structural resemblance to acetylcholine, and studies have shown that it has slight cholinergic properties. Acetylcarnitine was subjected to conformational analysis by extended Hückel theory (EHT) and complete neglect of differential overlap (CNDO/2) molecular orbital methods. The preferred conformations were examined with respect to their similarity to the Kier and Chothia-Pauling models of cholinergic receptor patterns. The preferred conformations of both isomers did not fit the receptor pattern described by Kier's model, although energy barriers to rotation are low enough to permit accommodation. The Chothia-Pauling model predicts activity for the S-isomer only. These studies partially explain the low cholinergic activity found for acetylcarnitine and the higher activity of (S)-acetylcarnitine compared to the R-isomer.