He was married three times and had two sons, Ivar Jerne (born 1936) and Donald Jerne (born 1941), with Tjek Jerne. He had a third son, Andreas Wettstein, with Gertrud Wettstein, in 1971. According to Söderqvist, his wife Tjek was distraught when she had found out that Niels was having an affair with her best friend, Adda Sundsig-Hansen. Tjek had told Adda about her own affairs, and Adda then told Neils about them too. After hearing this, Niels demanded a divorce. Tjek begged him to stay but he refused. She would then kill herself. Her son Ivar had woken up in the morning, smelled gas, and found his mother dead by the oven. His second wife was treated as a servant and nanny by Jerne. He was regularly unfaithful to his wives, and even though he was not physically handsome, he had attracted women by his charm as a conversationalist and his skills in the arts of love, which included a liking for sadism.