Thin basement membrane nephropathy (TBMN) is often attributable to mutations in the COL4A3 or COL4A4 genes that encode the α3 and α4 chains of type IV collagen, respectively, a major structural protein in the glomerular basement membrane. The aim of this study was to explore a new disease-related genetic mutation associated with the clinical phenotype observed in a Chinese Han family with autosomal dominant TBMN. We conducted a clinical and genetic study comprising seven members of this TBMN family. Mutation screening for COL4A3 and COL4A4 was carried out by direct sequencing. The RNA sequences associated with both proteins were also analyzed with reverse transcription PCR and TA cloning. The result showed that every affected patient had a novel heterozygous splicing mutation in COL4A4 (c.1459 + 1G > A), which led to the elimination of the entire exon 21 from the COL4A4 cDNA and resulted in the direct splicing of exons 20 and 22. This in turn caused a frameshift mutation after exon 20 in the open reading frame of COL4A4. In conclusion, we describe a novel splicing mutation in COL4A4 that results in TBMN. This analysis increases our understanding of TBMN phenotype-genotype correlations, which should facilitate more accurate diagnosis and prenatal diagnosis of TBMN.