Phallic malformations directly affect crocodilian copulatory function and thus could influence reproductive success in individual animals. This case series characterizes malformations observed and the implied reproductive consequences. A range of phallic malformations observed in saltwater crocodile (Crocodylus porosus), Nile crocodile (Crocodylus niloticus), broad-snouted caiman (Caiman latirostris), and Cuban crocodile (Crocodylus rhombifer) were assessed during veterinary examinations or postmortem studies; the observations were characterized into the following categories: amputation, phallic glans malformations, sulcus spermaticus obstruction, and prolapse. Through detailed descriptions of these anomalies, potential reproductive health effects based on current knowledge across crocodilian species is discussed. When considering captive management of breeding stock, it is vital to examine individual effectiveness at achieving proper intromission and insemination. Therefore, full reproductive examination in males should be part of routine examination to best care for individuals with such anomalies.