Herein we report the case of a 20-year-old woman who presented with multiple skin ulcers on her legs, severe pansinusitis, and chronic lung disease. She was initially thought to have Wegener's granulomatosis (WG). However, serologic studies indicated an HLA class I deficiency, which was confirmed by flow cytometry. Complementation studies and reverse transcriptase-polymerase chain reaction followed by direct DNA sequencing revealed a mutation in the gene encoding subunit 1 of the peptide transporter associated with antigen processing (TAP1). This mutation, which has not been previously described in the literature, results in a stop codon in the catalytic domain of TAP1. Although TAP mutations are rare, clinicians may encounter them in the evaluation of patients with suspected WG. In patients with WG-like symptoms it is important to consider this alternative genetic diagnosis as early as possible, not only so that appropriate antibiotic therapy can be initiated to prevent bronchiectasis, but also to avoid inappropriate immunosuppressive therapy that worsens the disease.