This paper presents a generalized job-shop problem taking into consideration transport time between workstations and setups machines in deadlock-free operating conditions. The automated transportation system, employing a number of automated guided vehicles is considered. The completion time of all jobs was applied as the optimization criterion. The created computational application was used to solve this problem in which chosen priority algorithms (FIFO, LIFO, LPT, SPT, EDD and LWR) were implemented. Various criteria were used to assess the quality of created schedules. Numerical results of the comparative research were presented for various criteria and rules of the priority