Trichophyton tonsurans is the primary etiologic agent of fungal infections in the pediatric population. Establishing techniques that facilitate strain discrimination offer the opportunity to investigate the relationship between fungal genotype, biochemical phenotype and disease presentation in the host. In the process of expanding efforts to elucidate intra-specific genetic variability in T. tonsurans, we have identified 2 genetic polymorphisms in the ALP1 gene: a fragment length polymorphism in the 5'UTR and a single SNP (G-->A) within the 3'UTR. Full sequence data revealed that the length polymorphism was constituted by a 16 bp repeat element, present in tandem from 3 to 6 times depending on the strain. Quantitative RT-PCR analysis demonstrated a clear association between the length polymorphism and ALP1 mRNA transcript levels. Not only do the sequence variations identified in this study increase our ability to discriminate T. tonsurans strains, but they also reveal the presence of a genetic variation with functional consequences at the transcript level that may play a role in regulating disease severity.