Madhyama Rasnadi decoction, one of the poly-herbal decoctions used in Ayurveda medicine is especially indicated for inflammatory conditions. The literature provides three different preparation methods of this decoction viz; Sri Lankan Traditional method (Method 1) and methods described in the texts Sharangadhara Samhita (Method 2) and Bhaishajya Ratnavali (Method 3). The aim of this study was to analyse and compare the phytochemical profiles of these three preparation techniques. Phytochemical profile analysis was carried out by (i) investigation of the extractable matter in 1 ml of decoction, (ii) development of Thin Layer Chromatography profiles and (iii) qualitative/quantitative determination of major phytoconstituents. Results revealed that the extractable matter of methods 1, 2 and 3 was 310±0 mg/ml, 420±0 mg/ml and 180±0 mg/ml, respectively. Differences (in terms of the number of spots and intensity) were observed in TLC fingerprint profiles, and phytochemicals such as phenols, tannins, flavonoids, saponins, alkaloids and terpenoids were present in all three types of decoctions. Gallic acid and quercetin were taken as standards to express the results of polyphenolic and flavonoid contents, respectively. Total polyphenolic contents of decoctions prepared according to methods 1, 2 and 3 were 121.68±0.60, 178.40±0.56, 86.20±0.25 mg gallic acid equivalents/g extract respectively. Total flavonoid contents of decoctions prepared according to methods 1, 2 and 3 were 69.45± 0.80, 129.30±0.65, 52.64± 0.50 mg quercetin acid equivalents/g extract respectively. In conclusion, more phytochemicals are concentrated on the decoction that made of method 2. The study opens more vistas of clinical applicability of Madhyama Rasnadi decoction, where further randomised case-control studies are needed.