For the short-term use of diesel engines, biodiesel can provide a comparable engine performance to that of using fossil diesel fuel. However, some arising problems including the reduction of the engine performance, the increase in lacquer deposits, and excessive carbon blacks in the combustion chamber and in the injectors resulting in an increase in the emissions and the damage to the engine have been indicated. Deposits formed inside or outside the injector may have an adverse influence on the engine performance and the fuel injection system. In this study, a review of the formed deposits in the injector of diesel engines fueled with biodiesel was conducted. The physicochemical mechanism of the deposit formation in the injector including injector nozzles, injector holes, and injector tips was mentioned. Moreover, the test-cycles for determining the deposit formation level in the injector were also introduced. Especially, the effects of the key factors such as biodiesel components, temperature, and injector configurations on the formation level of deposits were reviewed, and the utilization of the cativation mechanism in the controlling strategy of the deposits was presented. Besides, the impacts of deposits in the injector on the spray characteristics, combustion, and diesel engine operation process were also referred.