The present study is a comparison of the data of spectral analysis of heart rate variability with clinical evaluation of pathological state of doshas. The calculated cardiointervalography values are combined into three integral indexes, which according to the authors\' opinion reflect the influence on heart rhythm of vata, pitta and kapha, the regulation systems of the body 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 was collected from 42 participants to make the comparison with the clinical assessment of dosha imbalance. 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 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.