Pathological changes associated with CYN poisoning were reported to be in four distinct stages: inhibition of protein synthesis, proliferation of membranes, lipid accumulation within cells, and finally cell death. Examination of mice livers removed at autopsy showed that on intraperitoneal injection of CYN, after 16 hours ribosomes from the rough endoplasmic reticulum (rER) had detached, and at 24 hours, marked proliferation of the membrane systems of the smooth ER and Golgi apparatus had occurred. At 48 hours, small lipid droplets had accumulated in the cell bodies, and at 100 hours, hepatocytes in the hepatic lobules were destroyed beyond function.
The process of protein synthesis inhibition has been shown to be irreversible, however is not conclusively the method of cytotoxicity of the compound. Froscio et al.. proposed that CYN has at least two separate modes of action: the previously reported protein synthesis inhibition, and an as-yet unclear method of causing cell death.  It has been shown that cells can survive for long periods (up to 20 hours) with 90% inhibition of protein synthesis, and still maintain viability. Since CYN is cytotoxic within 16–18 hours it has been suggested that other mechanisms are the cause of cell death.
Cytochrome P450 has been implicated in the toxicity of CYN, as blocking the action of P450 reduces the toxicity of CYN. It has been proposed that an activated P450-derived metabolite (or metabolites) of CYN is the main cause of toxicity. Shaw et al.. demonstrated that the toxin could be metabolised in vivo, resulting in bound metabolites in the liver tissue, and that damage was more prevalent in rat hepatocytes than other cell types.
Due to the structure of CYN, which includes sulfate, guanidine and uracil groups, it has been suggested that CYN acts on DNA or RNA. Shaw et al.. reported covalent binding of CYN or its metabolites to DNA in mice, and DNA strand breakage has also been observed. Humpage et al. also supported this, and in addition postulated that CYN (or a metabolite) acts on either the spindle or centromeres during cell division, inducing loss of whole chromosomes.
The uracil group of CYN has been identified as a pharmacophore of the toxin. In two experiments, the vinylic hydrogen atom on the uracil ring was replaced with a chlorine atom to form 5-chlorocylindrospermopsin, and the uracil group was truncated to a carboxylic acid, to form cylindrospermic acid (Figure 6). Both products were assessed as being non-toxic, even at 50 times the LD of CYN. In the previous determination of the structure of deoxycylindrospermopsin, a toxicity assessment of the compound was carried out. Mice injected intraperitoneally with four times the 5-day median lethal dose of CYN showed no toxic effects. As this compound was shown to be relatively abundant, it was concluded that this analogue was comparatively non-toxic. Given that both CYN and epiCYN are toxic,  the hydroxyl group on the uracil bridge can be considered necessary for toxicity. As yet, the relative toxicities of CYN and epiCYN have not been compared.