The ICH and the PMDA published their guideline S5(R3) for the evaluation of reproductive toxicity of medicinal products, and has started to develop zebrafish developmental toxicity testing in Japan. In this study, we attempted to establish a zebrafish quality control protocol, which is the most important accuracy basis for the zebrafish developmental toxicity test. We first analyzed 12,906 fertilized eggs and found that 297 (2.3%) eggs died by 3 hours after fertilization. And 2,104 (16.3%) had morphological abnormalities by 3 hours after fertilization. By 24 hours after fertilization, 4,646 eggs (36.0%) were found to be dead. However, the survival rates from 1 to 5 days after fertilization were stable compared to the rapid decline in survival rate at 24 hours after fertilization. On the other hand, the results of time-lapse imaging from 3 hours to 5 days after fertilization showed that abnormal egg imaging at 3 hours after fertilization could predict death or morphological abnormalities up to 5 dpf. As a result, we report that it was possible to remove these low-quality fertilized eggs before the start of compound exposure (6 hpf) for developmental toxicity testing, thus reducing the frequency of false positives and enhancing the accuracy of zebrafish developmental toxicity screening.