Microbial contamination is the most important reason for losses in both scientific and commercial micropropagation systems. Latent and epiphytic bacteria can hitchhike imperceptibly during many subcultures. They reduce growth, multiplication and rooting or alter the response to in vitro plant growth regulators. In vitro plants, culture vessel, medium and possible endogenous bacteria release a set of volatile aromatic molecules (biogenic volatile organic compounds, BVOC). Because of its high throughput rate and extreme sensitivity, Selected Ion Flow Tube Mass Spectrometry (SIFT-MS) was chosen to distinguish between presumed clean and artificially Escherichia coli contaminated cultures of Ficus benjamina and Spathiphyllum wallisii. Contaminated cultures of F. benjamina and S. wallisii yielded a net BVOC fingerprint that was both different from each other and from the BVOC spectrum of E. coli. This suggests that they release volatiles that result from the specific interaction with E. coli. The availability of a true 100% bacteria free in vitro plant will be necessary to validate this technology for commercial use.