Improving throughput during high level synthesis includes determining a data dependency for a flow control construct of a high level programming language description and translating the high level programming language description into a circuit design specifying circuitry for implementation within an integrated circuit. The circuitry is pipelined. As part of the circuit design and using a processor, a stall detection circuit is generated. The stall detection circuit is coupled to selectively initiate a stall of a stalling portion of the circuitry according to the data dependency.