This paper examines the role of the microgenetic method in science education. The microgenetic method is a technique for exploring the progression of learning in detail through repeated, high-frequency observations of a learner's "performance" in some activity. Existing microgenetic studies in science education are analysed. This leads to an examination of five significant methodological issues in microgenetic research. Firstly, qualitative and/or quantitative approaches to data collection and analysis within the microgenetic approach are considered and a case is made for the appropriateness of qualitative microgenetic research. Secondly, it is argued that researchers may define static intervals, periods within which (for methodological purposes) change is assumed not to occur, when reporting microgenetic studies. Thirdly, researchers should consider providing justifications for their choice of sampling rate with reference to the rate of change of the phenomenon they are studying. Fourthly, the difficulty of distinguishing conceptual change from the existence of multiple understandings is highlighted. Finally, the nature of sequences of repeated measures in microgenetic studies is considered. It is argued that different methodological approaches are suitable for microgenetic studies of different phenomena and a list of guidelines for the use of the microgenetic method in small-scale, qualitatively analysed studies in science education is proposed.