The Cyathostominae are a complex group of nematodes and are the primary parasitic pathogens of horses. Little is known of their basic biology. As part of an investigation into mechanisms involved in reactivation of mucosal larval stages, we identified a gene encoding a predicted LIM domain-containing protein (Cy-LIM-1). LIM domains are cysteine- and histidine-rich motifs that are thought to direct protein-protein interactions. Proteins that contain these domains have a wide range of functions including gene regulation, cell fate determination and cytoskeleton organization. The Cy-lim-1 mRNA was identified as an abundant transcript following differential display-arbitrary primed reverse transcriptase-polymerase chain reaction amplification of RNA from faecal fourth stage larvae (FL4), which had been obtained from the diarrhoea of clinical cases of larval cyathostominosis. Detailed analysis showed that Cy-lim-1 was transcribed in FL4 and in other developmental stages; however there were differences in transcription of alternatively spliced variants amongst the stages. The predicted peptide sequence of Cy-lim-1 showed high identity to two LIM domain-containing proteins from Caenorhabditis elegans. RT-PCR analysis of these Cy-lim-1 homologues in C. elegans indicated that the two genes, which are described as separate entities in GenBank, are likely to compose a single gene of which alternative splice variants are transcribed. The LIM proteins from the cyathostomins and C. elegans were classified as LIM-only (LMO) proteins and, along with LMO proteins identified in sequence databases of other nematodes, comprise a group of LIM proteins distinct to those defined in other organisms.