Complement factor C4 exists as two main isotypes, C4A and C4B, with different functional properties and encoded by two separate genes. In addition, C4A and C4B genes can occur in multiple copies and may carry a retroviral HERV-K(C4) insertion in intron 9. To study association of C4 polymorphism with disease, accurate genotyping and phenotyping is important. However, current techniques are very laborious and not suitable to study large patient groups. Therefore, we aimed to develop novel assays for C4 geno- and phenotyping, to make high throughput possible. To study C4 gene copy number variation, a novel Multiplex Ligation-dependent Probe Amplification (MLPA) assay was set up with three synthetic probe parts. C4A and C4B protein levels were measured by isotype-specific ELISA's. The relationship between C4 genotype with C4A and C4B serum concentrations was examined in 104 healthy lab workers and 66 children with meningococcal disease. As expected, a strong positive correlation was found between C4A and C4B gene copy number and serum levels of total C4, C4A and C4B. In the healthy controls, 95.3% of C4A genes and 53.7% of C4B genes carried the HERV-K(C4) insertion. Presence of HERV-K(C4) resulted in less C4B protein expression, while there was no effect on total C4 levels. In the meningitis patients, no increased incidence of hetero- or homozygous deficiency of either C4A or C4B was found. In conclusion, the combination of MLPA and ELISA is very suitable to study the geno- and phenotype of complement C4 in large patient groups.