Variations in the rate of embryonic malformations of the anchoveta Engraulis ringens in a spawning area off central–southern Chile were assessed. Eggs in stages of development subsequent to blastodisc formation were collected and preserved. Several severe malformations were identified and grouped by: (1) proliferation of disorganized tissue in early and late developmental stages; (2) irregular blastopore closure; and (3) notochordal deformation, of which the second had the highest incidence among the embryos. The average rate of malformation was 5.64%, a value close to that reported for other Clupeiformes and below the rate of 10%, indicating the influence of purely endogenous factors. The expected relationship between temperature variations and malformation rates was not observed, probably because the natural temperature range experienced by the embryos was above that at which severe malformation had previously been observed in the laboratory. The relationship between egg size and malformation rates over the spawning season was not determined; however, a relationship between egg size and malformation rates was detected among the samples from each sampling date, which suggests that malformations may be attributable to endogenous factors rather than to environmental factors acting directly on the eggs in the plankton.