Semen analysis (SA) is considered mandatory for suspected male infertility although its clinical value has recently become questionable. Sperm motility is an essential parameter for SA, but is limited by high measurement uncertainty, which includes operator subjectivity. Computer-assisted sperm analysis (CASA) can reduce measurement uncertainty compared with manual SA. The objective of this study was to determine whether the Sperm Class Analyser (SCA) CASA-Mot system could reduce specific components of sperm motility measurement uncertainty compared with the World Health Organization (WHO) manual method in a single laboratory undertaking routine diagnostic SA. The study examined: (i) operator subjectivity; (ii) precision, (iii) accuracy against internal and external quality standards; and (iv) a pilot sub-study examining the potential to predict an IVF fertilisation rate. Compared with the manual WHO method of SA on 4000 semen samples, SCA reduces but does not completely eliminate operator subjectivity. Study SCA and CASA-Mot are useful tools for well-trained staff that allow rapid, high-number sperm motility categorization with less analytical variance than the manual equivalent. Our initial data suggest that SCA motility may have superior predictive potential compared with the WHO manual method for predicating IVF fertilization.