The relationship between complement factor H (CFH) and age-related macular degeneration (AMD) is very well known, but other genetic polymorphisms relating to AMD are more poorly understood. This study was designed to investigate the relationship between complement factor B (CFB) and early macular degeneration. Three hundred and forty-nine patients were recruited with early macular degeneration in at least one eye from Jules-Gonin University Eye Hospital in Switzerland. Patients were selected on the following criteria; early to intermediate AMD (International Classification and Grading System), no evidence of geographic atrophy or choroidal neovascularisation, over 50 years of age, no diabetic maculopathy, who could have adequate colour photographs of the macula taken, and they were also required to have a blood sample and to consent to the investigation. Severity of AMD was based on drusen size, total drusen, distribution, pigmentary abnormalities and presence of peripheral drusen. Genotyping for polymorphism CFB (R32Q, rs641153) was undertaken for all patients, with the majority being homozygotic for the major allele. This study demonstrated an association of CFB (polymorphism R32Q) with smaller drusen size and with smaller surface coverage by drusen. CFB (R32Q) was also associated with more peripheral drusen. The study is limited by a lack of demographic and environmental data concerning patients, which would clearly be relevant.