Light microscopic semen evaluation provides useful information about a given sperm sample, but due to its subjective nature has limited prognostic value for the reproductive performance of males or the outcome of assisted fertilization. Cryptic sperm abnormalities (occurring at the molecular level) are not easily detectable by light microscopy, but can be revealed by an array of biomarkers. The latter include fluorescent markers of acrosomal status, fluorochromes detecting altered sperm chromatin or DNA integrity, vital dyes revealing sperm mitochondrial activity, probes detecting apoptotic events, and antibodies detecting proteins that are either up- or down-regulated in defective spermatozoa. Many of the above biomarkers are best tested by flow cytometry, permitting rapid, automated, high throughput, objective measurement of the relative abundance of these biomarkers in semen. This review summarizes a strategy for the identification of novel male fertility/sperm quality biomarkers based on proteomic, biochemical and immunocytochemical analyses of defective spermatozoa. This approach identifies proteins or ligands uniquely associated with defective spermatozoa, regardless of whether they carry gross morphological defects or subtle, but critical hidden defects (e.g. DNA strand breaks) not detected with conventional, light microscopic analysis. Such markers, including ubiquitin, sperm thioredoxin SPTRX3/TXNDC8, 15LOX, and Lewis(y)-terminated N-glycans, are associated with poor semen quality and reduced fertility, warranting a designation of "negative" markers of fertility. The significance of sperm cytoplasmic droplet, a structure that accumulates several of the discussed biomarker proteins, is also discussed with regard to sperm quality and fertility.