Cyclodextrins (CDs) are widely used materials and still in the focus of drug development. In spite of the extensive studies, there is limited information about the cytotoxic effect of different derivatives. This study compares the cytotoxic effect of methylated beta-CDs and some ionic derivatives. The methylated CDs involved in this study differ in the number and position of the methyl substituents. Heptakis(2,6-di-O-methyl)-beta-CD (DIMEB) with a degree of substitution (DS) of 14 has two methyl groups in all of the seven glucose subunits mostly at O-2 and O-6 position, each OH group is methylated in heptakis(2,3,6-tri-O-methyl)-beta-CD (TRIMEB) (DS = 21), and an unsystematic substitution is realized in randomly methylated beta-CD (RAMEB). DS is defined as the number of substituents per cyclodextrin ring. Using the above definition, the DS for RAMEB is 12.6. To see the effect of the ionic groups an anionic and a cationic CD derivative were also investigated: (2-hydroxy-3-N,N,N-trimethylamino)propyl beta-CD (QABCD) (DS = 2) and carboxymethylated beta-CD (CMBCD) (DS = 3,5). The in vitro cell toxicity decreases in the order of DIMEB > TRIMEB > or = RAMEB > QABCD > CMBCD. Ionic beta-CDs were less toxic than the methylated derivatives.