T-cell immunoglobulin (Ig) and mucin domain-containing 1 (Tim-1) and Tim-4 are two members of the Tim family. In mammals, Tim-1 and Tim-4 are proteins mainly expressed in immune cells and are associated with immune response. In the present study, medaka Oryzias latipes' Tim-1 (OlTim-1) and OlTim-4 were identified and characterized using bioinformatics analyses. With the use of reverse-transcription polymerase chain reaction, the expression profiles of OlTim-1 and OlTim-4 were examined in embryos and adult fish and in immune tissues following the intraperitoneal injection of stimulants. The results revealed that OlTim-1 possesses a cytoplasmic region, a transmembrane region, a mucin domain, and an Ig-like domain, while OlTim-4 is composed of two Ig-like domains and a mucin domain, but without the transmembrane region and cytoplasmic region. OlTim-1 and OlTim-4 expressions are detectable from the gastrula stage on, indicating that they are zygotic genes. Furthermore, OlTim-1 and OlTim-4 are expressed ubiquitously in the adult. Administration of immune stimulants, namely lipopolysaccharides and polyinosinic:polycytidylic acid, significantly increased the expression levels of OlTim-1 and OlTim-4 in the liver and intestine within 1 day and in the head, kidney, and spleen within 3 to 4 days postinjection. These results suggest that OlTim-1 and OlTim-4 are possibly involved in both innate and adaptive immunities.