Functional genomic analysis of the mould pathogen Aspergillus fumigatus has identified multiple secondary metabolism genes upregulated in the host niche. Intriguingly, transcriptomic analyses of infectious germlings, germinating spores and mutants lacking the LaeA methyltransferase reveal differential expression of transposable elements (TEs), which often flank secondary metabolite gene clusters. In this study we investigate, in clinical and environmental isolates, the structure and distribution of a specific class of A. fumigatus long interspersed nuclear element (LINE)-like retrotransposons occupying subtelomeric loci in the A. fumigatus genome, and probe their stability in response to laboratory- and host-imposed stresses. In silico analyses revealed that this class belongs to the Tad clade of LINE-like elements. Southern blotting with a LINE-specific probe in clinical and environmental isolates revealed a high variability in the insertion pattern between strains and active transcription of LINE-like element(s) was discernable, in the type strain Af293, by RT-PCR. One out of 14 tested clinical isolates did not contain any LINEs at all, arguing against an absolute requirement for LINE-mediated activities in human infections. Finally, we found preliminary evidence of an association between mycovirus-infection and the expansion of Tad-element populations in discrete A. fumigatus genomes. (C) 2014 Elsevier Inc. All rights reserved.