This study reports a rare case of β(41/42,Cap)/β(A) genotype in a girl with β-thalassemia (β-thal) minor. The 13-month-old Chinese proband suffered anemia, diarrhea, stunted growth and emaciation. The routine polymerase chain reaction-reverse dot-blot (PCR-RDB) test result for β-thal mutations indicated that she was a compound heterozygote for β(41/42) and β(Cap). However, the complete blood cell (CBC) test gave the following results: mean corpuscular volume (MCV) 79.8 fL, mean corpuscular hemoglobin (MCH) 19.9 pg, with a Hb A2 value of 5.66%, suggesting that the proband also was β-thal minor. The proband's father showed typical microcytic hypochromic anemia characteristics with a decreased MCV and MCH (63.1 fL and 20.9 pg, respectively) and an increased level of Hb A2 (5.60%), while the proband's mother had normal levels of MCV, MCH and Hb A2. The PCR-RDB test result showed her father was also a compound heterozygote for the β(41/42) (HBB: c.126_129delCTTT) and β(Cap) (HBB: c.-11_-8delAAAC) mutations and her mother was normal. Finally, DNA sequencing identified that the β(41/42) and β(Cap) mutations of the proband were inherited from her father and located on one β-globin gene, suggesting that the proband's genotype is β(41/42,Cap)/β(A).