Held out wings (HOW) is an RNA-binding protein essential for spermatogenesis in Drosophila melanogaster . HOW is a signal transduction and activation of RNA (STAR) protein, regulating post-transcriptional gene expression. The characteristics of RNA-binding by the conserved short cytoplasmic isoform, HOW(S), are unknown. In vivo RIP-seq identified 121 novel transcripts bound by HOW(S) in germ stem cells and spermatogonia, many with signal transduction functions. (A/G/U)CUAAC motifs were enriched in 3’-UTRs and GCG(A/U)G in 5’-UTRs. HOW binds with high-affinity to sites containing CUAAC motifs from lola and hipk mRNAs. This study provides new insight into STAR protein-RNA interactions and functions in spermatogenesis.