Background Wegener's granulomatosis (WG), an autoimmune disease, is intimately associated with the sinonasal tract, with involvement reported in 85% of patients during the course of the disease process. The objective of this study was (1) to describe Lund-Mackay (L-M) scores, (2) to delineate patterns of neo-osteogenesis and bony erosion, and (3) to analyze the impact of surgery on the computed tomography (CT) findings of WG patients. Methods A retrospective review was performed on 74 patients with WG presenting to a tertiary care referral center. CT analysis was performed and graded by two independent reviewers. Results The mean age was 53 years with a male/female ratio of 0.6:1. The average L-M score was 10.0. Neo-osteogenesis was evident in 78% of the patients with overall average neo-osteogenesis score of 4.2 (range, 0–16). Bony erosion was noted on imaging in 62% of patients with overall average score for bony erosion of 2.0 (range, 0–8). Patients having undergone previous sinus surgery compared with no previous surgery had statistically significant elevation of overall L-M, bony erosion, and neo-osteogenesis scores (p = 0.024, 0.0009, and 0.0015, respectively). Conclusion CT imaging in WG patients shows elevated L-M scores and evidence of bony erosion and neo-osteogenesis. Furthermore, surgical manipulation in WG patients is associated with increased bony abnormalities and greater elevations of L-M scores, possibly because of worsening vasculitis and/or inflammation. The presence of concurrent neo-osteogenesis and bony destruction of the paranasal sinuses should raise clinical suspicion of WG in patients presenting with symptoms of chronic rhinosinusitis.