Abstract Interest in non-mammalian alternatives to in vivo animal teratogenicity testing has dramatically increased. However, few of these alternative screening systems have been critically evaluated or validated. In order to characterize such tests, there is a need for reproducible and standardized means of monitoring and scoring development. To address this need, a morphological scoring system was developed for medaka embryos. This paper presents this scoring system and demonstrates its application in developmental toxicity evaluations. Medaka embryos were collected within 2 h post-fertilization and cultured in Petri dishes in buffered saline until hatching. Thirteen developmentally different features were selected, and up to six morphological stages of each feature were defined and assigned scores of 0 to 5. Control as well as teratogen-exposed (methylnitrosourea, 1–10 mM) embryos were assessed. Morphological scores were calculated at 4 timepoints during development. Scores were significantly related to embryonic age and teratogen-exposed embryos showed dose-dependent decreases in mean score even at doses resulting in low malformation percentages. These results suggest that the use of such scoring systems in fish embryo cultures can provide a standardized index of embryonic development and aid in the detection of growth retardation and dysmorphogenesis. This will allow for quantitative comparisons of growth and development between experimental conditions and possibly to other embryo cultures (e.g., rodent) for which morphological scoring systems have already been established.