Sperm cells are variable both within and among species. To be able to accurately measure sperm cells and understand their function, it is important that sperm cells are preserved in a manner that maintains their structural integrity. Formalin is a widely used fixative and storage medium for sperm cells, but few studies have examined the effect of fixation and long-term storage on their morphological integrity. Ethanol is also a common fixation and storage agent for tissue samples, and here we examine if fixation and storage in formalin or ethanol alters sperm cell size and structural integrity. We found no significant effects of the fixation process on fresh sperm cells fixed in formalin or ethanol. Further, there were no consistent length changes in sperm cells stored in formalin or ethanol over a period of 227 days, or in sperm cells stored in formalin for three years. A comparison across 13–14 years of storage time showed a small but significant reduction in sperm cell length of 0.93%. Furthermore, sperm cells initially fixed in formalin remained quite stable in dry storage on glass slides for a minimum of six months (we found a mean reduction in sperm cell length of 0.18% after 6 months). The proportion of sperm cells with head damage was, however, much higher for samples stored in ethanol than for those stored in formalin. Overall, 70% of sperm cells had acrosome damage in ethanol versus only 3% in formalin. Finding intact sperm cells for measuring length, therefore, required greater effort in ethanol samples than in formalin samples. Our findings indicate that use of sperm cells from long-term storage for the study of sperm morphometrics is justified for either fixative, although formalin clearly preserves the sperm cells better.