In Indonesia, shallot cultivation finds difficulties to produce high viability seed. That low viability is caused by the abnormality of seed's structure. Normal shallot seeds have seed structure that consists of: testa, endosperm, and embryo. Normal embryo has curved shape which it has one cotyledon in endosperm. This research purpose is to find shallot viability and structure that is cultivated in tropic area, especially in Indonesia. This research is a deep observation research about water level, seeds viability and seeds structure monitoring by using microscope. To make a clearance about seeds structure composition, seeds are mixed with tetrazolium salt. Monitoring result shows that seed water level at harvest time is 18%, laid away at one month age is 13%, two months age is 12% and three months age is 10%. Seed viability at harvest until twenty nine days, seed that is germinated around 8%. At two months viability seed laid age until twenty two days is 36.6%. Meanwhile three months age laid viability test is done with germination boost compounding shows that IAA is able to fasten germination. At IAA treatment viability seeds are 17.25% that is followed with GA3 treatment around 13%. Another boosting substance that it's viability is only below 4%. Low viability is also proved by the seed structure. The result shows that mostly, the seeds has abnormal structure.