The document investigates how cis/trans isomerization impacts the in vivo distribution and clearance of two pairs of ozonide antimalarial drug isomers. In vitro experiments showed the trans isomers degraded more rapidly than the cis isomers in rat blood and liver microsomes, despite higher protein binding of the trans isomers. In vivo pharmacokinetic studies in rats demonstrated the trans isomers had approximately two-fold shorter half-lives and five to nine-fold higher unbound plasma clearance than the corresponding cis isomers. The results emphasize the importance of conformation in determining the in vivo properties of this class of antimalarial drugs.