He obtained a PhD in molecular medicine in 1981 from the University of Amsterdam[1] under Piet Borst with dissertation Trypanosomes: Kinetoplast DNA and Antigenic Variation.

He also clarified the complex genetic mechanism by which trypanosomes constantly change their surface antigens in order to escape the immune system.

He clarified the mechanism of nucleotide excision repair (NER) and associated hereditary diseases (xeroderma pigmentosum, Cockayne syndrome, trichothiodystrophy).

He found with Jean-Marc Egly that Transcription Factor II H (TFIIH) opens the DNA for the start of the NER.

[3] Hoeijmakers was elected in 2000 a member of the Royal Netherlands Academy of Arts and Sciences (section ‘Medicine’, dept.