Japanese quails (Coturnix japonica) were exposed in ovo to tris(1,3-dichloro-2-propyl) phosphate (TDCIPP; 500 ng/µl), Dechlorane Plus (DP; 500 ng/µl), or a 1:1 mixture of these two to investigate the effects on liver and thyroid gland morphology. Histological examination of 14-day-old quails showed that exposure to TDCIPP or the mixture induced hepatic sinusoidal dilatation. No marked effects were seen for DP alone. In addition, the mixture produced divergence of thyroid gland follicles and proliferation of follicular cells. Our study is the first demonstrating histopathological alterations as a result of exposure during early development to the flame retardants TDCIPP or a TDCIPP–DP mixture suggesting the need for further research efforts to investigate potential adverse health effects associated with exposure to these environmental chemicals in wild birds.