With the current assisted reproduction protocols, yolk-sac larvae of the European eel can be regularly produced. However, high mortality and deformity rates may exist during the first week after hatching with few larvae reaching the exogenous feeding stage. Recently, we suggested that larval survival could be impaired by pathogen pressure. Therefore, in this study, we tested the effects of antibiotics (rifampicin and ampicillin 50 mg L−1) and egg surface disinfection treatment (povidone iodine 25 ppm) on hatching success, larval survival and the occurrence of deformities in wild and feminized eels. Differences in egg quality aspects existed between offspring of wild and feminized eels. Eggs produced by the wild females were more buoyant than the ones released by the feminized eels. Larvae of the wild females hatched at higher rates and survived longer than the ones produced by the feminized eels. Disinfection treatment negatively affected hatching success and larval survival but the application of antibiotics improved larval survival. While larvae survived until 5 days post-hatch (dph) in the untreated controls, larvae continued to survive up to 21 dph when treated with antibiotics. Despite the beneficial effects of antibiotics on larval survival, a wide diversity of deformities could be observed during early development of eels that have not been reported before. The deformity determination key for young eel larvae that is presented in this paper fills a gap in the knowledge about larval deformities during early ontogeny. The larvae showed pericardial oedemas, microcephaly, an enlarged-yolk sac, necrosis and notochord deformities. The treatment with antibiotics decreased the deformity rates although they remained high (75–85%). The causes behind each deformity need to be clarified in order to prevent them in future trials.