Over the last decade, modified oligoribonucleotides have emerged as a valuable tool in catalytic RNA studies. The range of incorporated nucleotide analogues includes modifications in the base, sugar or phosphate moieties. The comparisons of the properties of the modified RNA enzymes with unmodified models allow one to draw the conclusions concerning the importance of specific functional groups within the catalytic RNA. In this review, we discuss the selected examples of modified oligonucleotides applications to investigate some aspects of mechanisms and structure/function relationships of small ribozymes (hammerhead and hairpin). The importance of modifications for the improvement of ribozyme catalytic activity and resistance to nucleases are also presented.