A scheduling system is proposed and developed for a special type of flow shop. In this flow shop there is one machine at each stage. A job may require multiple operations at each stage. The first operation of a job on stage j cannot start until the last operation of the job on stage j -1 has finished. Pre-emption of the operations of a job is not allowed. The flow shop that the authors consider has another feature, namely time lags between the multiple operations of a job. To move from one operation of a job to another requires a finite amount of time. This time lag is independent of the sequence and need not be the same for all operations or jobs. During a time lag of a job, operations of other jobs may be processed. This problem originates from a flexible manufacturing system scheduling problem where, between operations of a job on the same workstation, refixturing of the parts has to take place in a load/unload station, accompanied by (manual) transportation activities. In this paper a scheduling system is proposed in which the inherent structure of this flow shop is used in the formulation of lowerbounds on the makespan. A number of lowerbounds are developed and discussed. The use of these bounds makes it possible to generate a schedule that minimizes makespan or to construct approximate solutions. Finally, some heuristic procedures for this type of flow shop are proposed and compared with some well-known heuristic scheduling rules for job shop/flow shop scheduling.