Familial Mediterranean fever (FMF) is an autosomal recessive disorder characterised by recurring attacks of fever and serositis. Five sequence alterations (M694V, V726A, M680I, M694I and E148Q), in the MEFV gene, account for the majority of FMF chromosomes. The wide clinical variability of the disease has been related to MEFV allelic heterogeneity. M694V homozygotes have a severe form of the disease. Mutations E148Q and V726A have reduced penetrance. The clinical features, associated with the M680I and the complex V726A-E148Q allele, are not well defined. This study aims to further characterise the phenotypic profile associated with the major MEFV mutations. We investigated 220 FMF patients, in whom both FMF alleles have been identified, and found that different genotypes are characterised by a specific allelic related clinical profile and penetrance. Homozygotes for the M694V mutation and the complex V726A-E148Q allele are the most severely affected and often endure renal amyloidosis. Homozygotes for the M680I and V726A alleles and compound heterozygotes for either the M694V or the V726A-E148Q alleles in combination with either the E148Q, the V726A or the M680I alleles are significantly less severely affected. The morbididity associated with the complex V726A-E148Q allele by far outweighs that associated with the V726A allele, bearing evidence to the fact that the E148Q mutation is not a benign polymorphism. These findings increase our understanding of the role of allelic variability in disease expression.