We compared the effects of four quaternary benzo[c]phenanthridine alkaloids, i.e., chelerythrine, chelilutine, sanguinarine and sanguilutine, and two quaternary protoberberine alkaloids, berberine and coptisine, on the human cell line HeLa (cervix carcinoma cells) and the yeasts Saccharomyces cerevisiae and Schizosaccharomyces japonicus var. versatilis. The ability of alkaloids to display primary fluorescence, allowed us to record their dynamics and localization in cells. Cytotoxicity, anti-microtubular and anti-actin effects in living cells were studied. In the yeasts, neither microtubules nor cell growth were seriously affected even at the alkaloid concentration of 100 mg/mL. The HeLa cells, however, responded to the toxic effect of alkaloids at concentrations ranging from 1-50 mg/mL. IC50 values for individual alkaloids were: sanguinarine IC50 = 0.8 mg/mL, sanguilutine IC50 = 8.3 mg/mL, chelerythrine IC50 = 6.2 mg/mL, chelilutine IC50 = 5.2 mg/mL, coptisine IC50 = 2.6 mg/mL and berberine IC50 =10.0 mg/mL. In living cells, sanguinarine produced a decrease in microtubule numbers, particularly at the cell periphery, at a concentration of 0.1 mg/mL The other alkaloids show the similar effect but at higher concentrations (5 to 10 mg/mL). The strongest effects of sanguinarine were explained as a consequence of its easy penetration through the cell membrane due to non-polar pseudobase formation and to a high degree of molecular planarity.