In Ayurveda, a healthy body is defined by a balance among the three doshas (Vata, Pitta, Kapha) and ailments result due to imbalances among them. It prescribes specific plant parts/tissues collected in a season-specific manner for curing dosha-related imbalances but the plants prescribed for treating a particular dosha imbalance belong to taxonomically diverse families and often contain similar classes of phytomolecules, making it difficult to provide a phytochemical validation for any similarity that might exist among them. This exploratory study hypothesised that plants of the same dosha-curing group may have similarity at the transcript level. For proving/disproving the hypothesis, cDNA-AFLP and specific expression subset analysis (SESA) were carried out on the Ayurveda-defined active tissues of four representative plants each of the three dosha-balancing groups. cDNA-AFLP analyses indicated that even though the plants belonging to a particular dosha-group may widely differ at the transcript level, there is a small fraction of transcripts that is monomorphic among their active tissues. SESA (Tester-active tissue cDNA; Driver-cDNA from other major tissue[s]) generated 803 subtractive ESTs from the twelve plants that yielded 150 unigenes upon assembly (of ESTs from each plant separately). Cross-plant EST assembly for plants in the same dosha group also corroborated the results. Although a distinct pattern of transcripts was not observed across all the plants in a particular dosha group, some commonalities were obtained that need further characterization towards searching for the hitherto elusive similarity among plants of the same group.