Commercial lipases from the yeast Candida rugosa have been compared with two recombinant C. rugosa lipases, rCRL1 and rCRL1lid3, with respect to their immobilization and exploitation in biotransformations aimed at the synthesis of pyrimidine nucleosides. Immobilization on octyl-agarose and decaoctyl-Sepabeads but not on Eupergit ® C gave comparable results to commercial lipases for rCRL1, while only a low percentage (12%) of rCRL1lid3 was efficiently immobilized. When immobilized on decaoctyl-Sepabeads, rCRL1 showed a markedly higher stability to chemical inactivation, since it could maintain 100% activity after 180 h incubation in 30% (v/v) acetonitrile. Hydrolysis of peracylated uridine and cytidine and their fluorinated counterparts proceeded with high regioselectivity and good yield, and even improved when rCRL1 was immobilized on decaoctyl-Sepabeads.