Normal (n = 20) and abnormal (n = 21) semen samples were explored for possible relationships between conventional semen parameters, chromatin status, and microdeletions in the Y chromosome. DNA fragmentation was detected by the terminal deoxynucleotidyl trasferase-mediated dUTP-nick end labelling (TUNEL) assay, chromatin condensation, and DNA packaging quality were assessed by chromomycin A3 (CMA(3)) staining. All men were investigated for Y chromosome microdeletions using polymerase chain reaction (PCR). No deletions were detected in 21 severely oligozoospermic men for the three screened regions (AZFa, AZFb, and AZFc). Men with normal semen parameters showed better chromatin condensation. Spermatozoa with low motility were more likely to contain loosely packaged chromatin. In the abnormal semen group, DNA fragmentation (TUNEL) correlated significantly with sperm motility, concentration, and chromatin packaging assessed by chromomycin A3. However sperm morphology did not correlate significantly with TUNEL and CMA(3) staining.