The present study compares the major (finger, sorghum, pearl) and minor millet flours (barnyard, foxtail, kodo, little, proso) with wheat flour for their nutritional (proximate, mineral and polyphenolic content), antinutritional, functional, morphological, and pasting properties. The millet flours protein content varied from 13.71-6.39g/100g, followed by ash content varied from 2-1.02%, lipid varied from 1.62-5.68%, carbohydrate 67.78-73.70%, crude fibre 0.92-4.77g/100g and moisture 9.45-12.69% as compared to the wheat flour having 12.07g/100g, 1.22%, 1.67%, 71.89%, 2.26g/100g and 10.89% respectively was determined using official protocols of AOAC (Association of official analytical chemists). Calcium was found to be significantly higher in finger millet flour 87.02mg/100g. Atomic spectrometer, rapid-visco analyser (RVA), fourier transform infra- red spectroscopy (FTIR), scanning electron microscope (SEM) and differential scanning calorimeter (DSC) was used to measure minerals, pasting, functional, morphological and thermal properties respectively. The raw millet flours showed good pasting properties as in barnyard millet flour with 1216 cp peak viscosity and pearl millet flour having 88.05°C pasting temperature which is approximately similar to the wheat flour used as control. The highest total phenolic content was found to be in finger millet flour i.e. 1318.12 mgGAE/100g. The antinutritional factors namely tannin and phytic acid was lowest found to be in foxtail millet flour 8.03mg/100g and 0.37mol/g. Functional properties such as water holding capacity was found to be good in finger millet flour (3.12g/g) and oil holding capacity was good kodo millet flour (2.50g/g), the foaming capacity was good in barnyard (4.11%) whereas dispersibility was good in little millet flour (85.02 g/ml) compared to wheat flour. The FTIR revealed the presence of amide group and the presence of starch protein complex. The thermal analysis showed the presence of higher amounts of proteins and lipids in the minor millet flours. Significant differences (p≤0.05) were also determined in most of the values of the millet flours. This present work on comparative study would contribute to reduce risk of over-reliance on staple gluten containing cereals, and to formulate and optimize healthy food products of different preferences from the above-mentioned gluten free nutritive flour in combinations or as alone.