The individual rearing method using tissue culture microplates is useful for assessing fertility, hatchability, and larval survival in the Japanese eel Anguilla japonica. However, the rearing water needs to contain chemicals to suppress surface tension-related death that occurs upon hatching and antibiotics to prevent bacterial proliferation. To apply this method for assessing the occurrence of morphological deformities, it is essential to ensure that these additives do not induce malformations. Fertilized eggs were individually stocked in 48-well plates and reared until completion of yolk absorption. Polyethylene glycol 6,000 (PEG 6,000), bovine serum albumin (BSA), and an antibiotic solution containing penicillin G potassium (200,000 IU/ml) and streptomycin sulfate (0.2 g/ml) were added to the rearing water at various concentrations. PEG and BSA fully suppressed surface tension-related death at 1μg/ml and above without induction of dose-dependent malformations. The antibiotic solution fully prevented bacterial proliferation at 0.25μl/ml and above and did not induce dose-dependent malformations at 1μl/ml and below. However, it tended to increase the spinal curvature at 2.5μl/ml and above. We conclude that the individual rearing method can be applied to assess morphological deformities in eel larvae at the yolk absorption stage with minimum use of these additives within their effective concentrations.