Lentil and horse gram germplasm was assessed for variety in seed and flour properties. Horsegram grains showed higher a* and b* and lower L* values as compared to lentil grains indicating lentil grains were lighter in color as compared to horse gram. Both the pulses showed significant differential accumulation of minerals. Flours from horse gram lines showed higher Mn, K, Mg, Na, Zn and Ca content and lower Cu and Fe content as compared to lentil lines. Polypeptide of 42 kDa was present in IC94636 and IC139555 only and 35 kDa PP subunit was absent in all the horse gram lines except IC94636. Major polymorphism among lentil lines was observed in 10, 35-37 and 55-49 kDa PP subunits. Amount of b-sheets and b-turns was the highest whereas that of antiparallel b-sheets was the lowest. NIC17550, NIC17551 and NIC17552 showed higher content of antiparallel b-sheets and random coils among lentil lines. PL1 showed the highest portion of ahelixes and b-turns whereas PL57 showed the highest proportion of b-sheets among lentil lines. Lentil flours showed higher proportion of aspartic acid, glutamic acid, asparagine, serine, citrulline and serine and lower proportion of histidine, threonine, GABA, tyrosine and cystine as compared to horse gram.