<i>Background:</i> Fuchs heterochromic cyclitis (FHC) is a chronic inflammatory eye disease, usually presenting as unilateral anterior uveitis. Up to date no disease susceptibility genes have been described for FHC. <i>Methods:</i> The allele frequency of HLA DRB1 and DQB1, polymorphisms of the tumour necrosis factor (TNF) α promoter region (–376, –308, –238), the promoter (–318), first exon (+49) and (AT)n repeat polymorphism of the cytotoxic T cell antigen 4 (CTLA4) gene were analysed in 44 FHC patients and 139 healthy controls. <i>Results:</i> The CTLA4 –318 C/T genotype was increased in FHC patients [odds ratio (OR) 3.0, 95% confidence interval (CI) 1.4–6.5], as well as long CTLA4 (AT)n microsatellite alleles with more than 16 AT repeats (OR 2.6, 95% CI 1.3–5.3). A trend towards the –308 G/A <i>TNF</i>-α genotype was found in the patient cohort, whereas no difference in HLA class II allele distribution was observed. <i>Conclusion:</i><i>CTLA4</i> but not TNF-α or HLA class II DRB1 and DQB1 may represent a candidate gene for disease susceptibility in FHC.