The current investigation was carried out in 2016 and 2017 in the Tissue Culture Laboratory of the Department of Vegetable Crops and Biotechnology Laboratory of the Department of Genetics, the Faculty of Agriculture, Assuit University, using the potato cv. Cara. The study assessed the phonotypical alterations and genetic stability using molecular analyses (RAPD, ISSR and SRAP). The stem single node cultures of potato cultivar 'Cara' were followed-up for three shoot multiplication cycles (subcultures) on the medium supplemented with 0.5 or 1.0 mg/l benzyl adenine (BA) or lacking the BA. Shoots on BA containing medium as compared to that on the medium lacking BA were shorter, developing multiple shoot branches and producing larger number of stem nodes/culture. The stem nodal yield increased by 87.5% and 131.3% in cultures on medium supplemented with 0.5 and 1.0 mg/l BA, respectively. Cultures of nodal explants derived from shoots propagated on BA containing medium exhibited an interrupted root formation. No roots formed after the second shoot multiplication cycle using nodal explants from shoots formerly grown on medium with 1.0 mg/l BA. In the third shoot multiplication, cycle rooting did not occur using nodal explants from shoots harvested from cultures on medium with 0.5 or 1.0 mg/l BA. The molecular assay was confirmatory to the phenotypic assay and the different marker methods used were reliable in assessing tissue culture-induced variations. Overall results are against in vitro use of BA in potato cv. Cara transplant-production media. Check of genetic stability at close intervals is advisable.