The volume and complexity of commercial bioreactors for sterile hydroponics and hairy roots are too large for comparative analysis of many cultures. Here a small-scale bioreactor fabricated from standard glass materials and suitable for both airlift and bubble aeration mode is described. The performance of the bioreactor was tested by growing oilseed rape (Brassica napus L.) and rose plants (Rosa canina L.) in sterile hydroponics and by cultivating hairy roots of henbane (Hyoscyamus niger L.) and sesame (Hyoscyamus niger L.). Plants grown in hydroponics for up to six weeks did not show chloroses or necroses. Hairy roots grew faster or comparably fast in bioreactors as compared to shaking flasks. Root exudates of roses and exudates of hairy roots of henbane were subjected to targeted and nontargeted analysis by HPLC coupled with optical and mass spectrometric detectors. The diversity and concentration of hairy root exudates were higher in bioreactors than in shaking flasks. The composition of hairy root exudates of three accessions of H. niger did not match the genetic relatedness among the accessions. Hairy roots of Hyoscyamus niger exuded salicylic acid in amounts varying among plant accessions and between bioreactors and shaking flask cultures.