Marie-Claire Alain was born in Saint-Germain-en-Laye on 10 August 1926. Her father Albert Alain (1880–1971) was an organist and composer, as were her brothers, Jehan (1911–1940) and Olivier (1918–1994). She began assisting her father when he played organ in the parish church at the age of 11. She studied at the Paris Conservatory in the organ class of Marcel Dupré, where she was awarded four first prizes. She also studied harmony there with Maurice Duruflé.