Context and setting Including the practical task of karyotyping into cytogenetics courses yields several potential didactic advantages. Students are challenged to apply their knowledge of the regular karyotype in order to recognise numerical or structural chromosome aberrations. At the same time, the activity provides a first-hand experience of the intricacies of karyotyping when matching highly variable homologue chromosome pairs. Why the idea was necessary Students expressed their dissatisfaction with the cumbersome cutting of chromosomes from printed photomicrographs, inherent to the conventional cardboard-based fashion of the exercise, especially having learned about interactive computer-based karyotyping in routine diagnostic laboratories. What was done A specialised e-learning application was developed based on the Mozilla Application Framework to simulate the rearrangement of randomly distributed sets of chromosomes. Mouse movements permit the interactive translation and rotation of single chromosomes. An optional scheme, which graphically matches the accepted Denver classification of human mitotic chromosomes,1 can be superimposed onscreen. Students can have their proposed solutions independently verified with a ‘solve’ option from the program menu. The fraction of appropriately sorted chromosomes is then displayed and incorrect choices are highlighted with coloured labels. More specific clues on faulty positioning and rotation can be overlaid with coloured arrows which illustrate the mapping required to achieve correct chromosome placement. Currently, the software allows seven prepared chromosome sets to be processed, reflecting both normal cases and common chromosomal aberrations. All chromosome edges were predefined within the program, so users were spared the previous drudgery of scissoring. Medical students were prompted to use the application as part of their mandatory cytogenetics tuition, following a lecture about indications for cytogenetics, karyotyping methods, and chromosome morphology concentrating on highly specific landmarks. Evaluation of results and impact In two consecutive semesters 113 of 250 participants, who had used the application alone or in teams mostly of two or three, anonymously completed a voluntary questionnaire that consisted of three multiple-choice items and a free-text field. Almost every responder (94%) agreed with the assertion that the software was ‘either intuitively usable or easy to learn’ (4% disagreed). A total of 42% of respondents agreed that using the software ‘enhanced their learning success’ (24% disagreed and 34% were neutral or undecided) and 73% recommended ‘integrating the application in future courses’ (7% disagreed and 20% were undecided). Further comments included requests for the system to be made more responsive (which may in the future be addressed by the application of more powerful hardware), a suggestion to extend the software to allow for practice of cytogenetic nomenclature, as well as a proposal to provide touch-screen displays. These results indicate that software-based chromosome sorting may constitute a viable component of teaching cytogenetics.