Background Mutations in the hepatocyte nuclear factor-1A gene cause the type 3 form of maturity-onset diabetes of the young (MODY3). This study was undertaken to determine mutations and sequence variations of the HNF-1A gene in Chinese with familial early-onset and/or multiplex diabetes mellitus. Methods We screened all ten exons of the HNF-1A gene, including exon/intron junctions, by direct sequencing in 272 unrelated Chinese, including 80 healthy controls and 192 probands of early-onset and/or multiplex diabetes pedigrees. Results In addition to one silent mutation of c.864 G >C [p.G288G] in exon4 at codon 288, which had been reported previously, a total of four novel mutations including two missense mutations (c.245C>T [p.T82M] and c. 390 G > T [p.Q130H]) and one frameshift mutation P353fsdelACGGGCCTGGAGC and one silent mutation c.759 G > T [p.G253G] were identified. Moreover, eleven substitutions were identified in 192 probands. Of these, three variants (-8 G>A, -128 T>G and IVS2+21 G>A) were not observed in 80 healthy controls and one of them (-8 G>A) was not reported previously and the two promoter variants co-segregated with diabetes. The genotype and allele frequencies of the other eight variants in the diabetic patients were not significantly different from those in the healthy controls. No significant relationships were observed between the eight variants of the HNF-1A gene and clinical variables (plasma glucose, insulin, C-peptide and fasting lipid profile). Conclusion The prevalence of structural mutations in the HNF-1A gene responsible for familial early-onset and/or multiplex diabetes appears to be rare among Chinese patients. Background Mutations in the hepatocyte nuclear factor-1A gene cause the type 3 form of maturity-onset diabetes of the young (MODY3). This study was undertaken to determine mutations and sequence variations of the HNF-1A gene in Chinese with familial early-onset and / or multiplex diabetes mellitus. Methods We screened all ten exons of the HNF-1A gene, including exon / intron junctions, by direct sequencing in 272 unrelated Chinese, including 80 healthy controls and 192 probands of early-onset and / or multiplex diabetes pedigrees. Results In addition to one silent mutation of c.864 G> C [p.G288G] in exon4 at codon 288, which had been reported previously, a total of four novel mutations including two missense mutations (c.245C> T [ p.TQ130H]) and one frameshift mutation P353fsdelACGGGCCTGGAGC and one silent mutation c. 759 G> T [p.G253G] were identified. Furthermore, eleven substitutions were identified in 192 probands. Of these, three variants (-8 G> A, -128 T> G and IVS2 + 2 1 G> A) were not observed in 80 healthy controls and one of them (-8 G> A) was not reported previously and the two promoter variants co-segregated with diabetes. The genotype and allele frequencies of the other eight variants in the diabetic patients were not significantly different from those in the healthy controls. No significant relationships were observed between the eight variants of the HNF-1A gene and clinical variables (plasma glucose, insulin, C-peptide and fasting lipid profile). Conclusion The prevalence of structural mutations in the HNF-1A gene responsible for familial early-onset and / or multiplex diabetes appears to be rare among Chinese patients.