Despite the fundamental importance of transcription start sites (TSSs), little is known about TSSs in C. elegans. This is due to the high frequency of trans-splicing of C. elegans mRNAs, a process which post-transcriptionally removes RNA segments of variable length from the 5'end of mature mRNAs. WormTSS is a comprehensive collection of TSSs for trans-spliced genes generated from the sequencing of Illumina reads from pre-trans-splicing 5'-ends that were captured using a modified 5'-SAGE procedure. Our data provides an enabling resource for both experimental and theoretical analysis of gene structure and function in C. elegans.