Snouck was surrounded by women all his life. His father died when he was just 13 years old. His mother was the most important woman in his life, and she did everything possible to enable her son to study and moved to Leiden for him. His sisters Jacqueline and Catootje also lived there. In the Dutch East Indies, Snouck first lived in a house in the native kampong behind the Kramat neighbourhood and later in a large house in the Parapatan district on the Djalan Kampong Lima (later called the Oude Tamarindelaan and now the Jalan Wahid Hasyim). This was where he lived with his wife Sangkana, the daughter of the chief penghulu of

Ciamis, Haji Muhammad Ta'ib. They got married in 1889 but Sangkana died in childbirth in October 1895. He later married Siti Sadijah (Buah), who was 28 years younger. Snouck had a total of five children with the two women. He lived his life in the Indies emphatically as a Muslim and did not drink alcohol or eat pork. When he left for the Netherlands in 1906, he left his Indonesian family behind on Java. Once in the Netherlands, Snouck married Ida Oort, and their daughter Christien was born in 1914.