Selection strategies developed in microbial genetics were successfully extrapolated to in vitro cell culture systems of higher plants and are having a major impact in the elucidation of regulatory mechanisms of basic cellular processes in eukaryotes. Although an increasing number and wide spectrum of biochemical variants have been isolated in such cell culture systems, their routine selection, characterization, and manipulation have not yet been achieved. Methodological limitations are considered to be one of the major reasons. Suspension or callus cultures, so extensively employed during the last decade in mutation-selection experiments and so useful in demonstrating the potentialities of in vitro screening techniques in obtaining various biochemical markers, have inherent drawbacks which limit in our opinion their further contribution in this field. Protoplast cultures represent an ideal tool for mutation and selection experiments. It is the purpose of this review to show how, due to recent methodological advances in the manipulation of some model protoplast culture systems, essential aspects of mutagenesis and selection of biochemical mutants can be reconsidered. These systems are simple and efficient, and lend themselves to statistical interpretation. Genetic analysis of selected variants should help us to understand and define better the new set of problems and concepts revealed by the somatic cell genetics of higher plants; combined with biochemical analyses it should elucidate the basic relationship between control of biological processes at cellular and whole organism level.