There have been several reports suggesting that the deficiency of complement 4 (C4) and/or deletion of C4 genes are the genetic risk factors in patients with IgA nephropathy (IgAN) and Henoch-Schönlein nephritis (HSN). In the current study, we tried to clarify the genetic structure of deleted C4 genes as well as the isotype deficiency of the patients. Also, we investigated the DQB and DRB genes which are located near the C4 genes to identify a possible linkage and to find the associated allele. Our results showed that locus II deletion of C4, not the C4B sequence loss, is a risk factor for these diseases and the deleted gene can be either C4A or C4B. There was no specific isotype deficiency or specific allotype which was significantly increased or decreased in the patients. But, there was an increased frequency of DQA1*0301 gene in the patient group (corrected p = 0.04), which suggests that DQA1*0301 as well as C4 gene deletion could be genetic risk factors for these diseases.