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Introduction Plants from Amaryllidaceae family are of interest since they produce a particular type of alkaloid useful for the treatment of neurodegenerative diseases of the central nervous system, such as Galanthamine. Given the low content of these secondary metabolites in the plant, it is necessary to study mechanisms to increase the productivity of them. Objective To obtain fast qualitative and quantitative analysis of the alkaloids and extend the understanding of biosynthesis and metabolism in these kinds of plants. Furthermore, establish a reliable, simple and fast analytical method for the in vitro callus culture of vegetative organs for Rhodophiala pratensis species. Methods The alkaloids composition of the callus culture of R. pratensis were analysed by gas chromatography coupled with mass spectrometry (GC–MS). Results A methodology for the qualitative and quantitative analysis of the alkaloids present in fresh callus culture of this wild plant species was established. The analysis showed alternation in the alkaloids type ratio and number of compounds between wild bulbs, in vitro bulbs and callus. It was possible to identify 24 alkaloids from a pool of 60 signals whose fragmentation pattern corresponds to the alkaloids of Amaryllidaceae plants. Together with the aforementioned, the amount and type of alkaloid present in the plant material obtained by in vitro culture of R. pratensis was determined in the same way. The results show the high biosynthetic potential of in vitro grown bulbs and callus tissue that are able to produce significant amounts of pharmacologically relevant alkaloids from R. pratensis in various proportions that depend on the culture conditions such as supplementation with growth substances. The in vitro grown bulbs produce an alkaloidal extract that contain a 52.6% w/w of alkaloids. Conclusion This study allowed the alkaloid content in callus culture of R. pratensis to be found by means of GC–MS. These results allowed a relationship between the type of growth regulator and the type of alkaloids found to be established. Finally, we can say that the results achieved to state that the production of alkaloids using different combinations of growth regulators could be directed during in vitro micropropagation from provided plant material.