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The use of automatic repeat and request (ARQ) systems have become widespread in the HF community because they can provide "error-free" data delivery over unreliable links. STANAG 5066 (S _5066) is an ARQ protocol which was adopted as the official NATO interoperable ARQ protocol for use on HF by NATO Allied forces. S_5066 is an adaptive ARQ system and one of its goals is to maximize throughput. In order to accomplish this, algorithms that select on-air data rate and interleaver size for a given channel condition are required. This paper investigates the throughput performance of S_5066 when utilizing STANAG 4539 (S_4539) high data rate (HDR) HF waveforms. Several HF channels are considered in order to determine which data rate and interleaver size provides the best performance for the particular channel condition. A set of recommendations is also provided to assist S_5066 ARQ designers in developing algorithms to select the appropriate data rate and interleaver size.