This study compares the spectral analysis data of heart rate variability with clinical evaluation of the pathological state of doshas. The calculated cardiointervalography values are combined into three integral indexes, which, according to the authors’ opinion, reflect the influence on the heart rhythm of vata, pitta, and kapha, the body’s regulation systems known as doshas in Ayurveda. Seven gross dosha imbalances were assessed to test the agreement between the two methods in this study. Heart Rate Variability (HRV) spectral data were collected from 42 participants to compare with the clinical assessment of dosha imbalance. The clinical method of dosha assessment and method of calculating integral indexes by cardiointervalography data showed substantial agreement by Kappa coefficient statistic (k = 0.78) in the assessment of gross dosha imbalance. The results of the data generated from this pilot study warrant further studies to rigorously validate the algorithms of HRV analysis in understanding dosha imbalance in Ayurvedic clinical practice and research settings. This study was funded by Biokvant, Russia.