Functional sperm tests such as the sperm chromatin structure assay (SCSA), chromomycin A3 staining (CMA(3)) and hyaluronic acid binding assay (HBA) have been suggested as predictive tests of fertility in vitro. This study aimed to define the clinical role of these functional parameters in assisted reproduction in a prospective cohort study. Conventional sperm diagnosis (motility, morphology and concentration) as well as SCSA, CMA(3) and HBA tests were performed on 205 semen samples [74 IVF, 94 ICSI and 37 combined IVF/intracytoplasmic sperm injection (ICSI)]. Main outcome parameters were fertilization rate, clinical pregnancy rate and take-home baby rate. The study showed that each of the three functional sperm tests was related to one or more conventional and one or more functional sperm tests, indicating that spermatozoa from patients with abnormal conventional semen parameters have a higher likelihood for multiple functional abnormalities. Only SCSA and CMA(3) staining were shown to have a limited predictive value when IVF or combined IVF/ICSI was applied. The proposed threshold value of <or=15% for predicting good fertilization rates and obtaining a pregnancy in IVF could only be confirmed for percent HDS (high DNA stainability in SCSA). ICSI outcome was not influenced by any of the conventional or functional sperm parameters.