Human sperm morphology has been described as an essential parameter for the diagnosis of male infertility and a prognostic indicator of natural or assisted pregnancies. Nevertheless, standard morphological assessment remains a subjective analysis and its impact on intracytoplasmic sperm injection (ICSI) is also of limited value. The objective of this prospective cohort study was to investigate whether motile sperm organelle morphology examination (MSOME) can improve semen analysis by better defining male infertility and providing a better prognosis for ICSI up to a year later. Data were obtained from 483 patients undergoing conventional semen analysis from June 2015 to June 2017 in a private university-affiliated in vitro fertilization (IVF) center. The correlation of MSOME with seminal parameters was evaluated. One hundred and thirty patients underwent ICSI up to a year later, and the correlation between MSOME and ICSI outcomes was established. Except for volume, all seminal parameters were positively correlated with MSOME I+II. MSOME was also distinct between World Health Organization (WHO) classification groups, with normozoospermic and oligoasthenoteratozoospermic presenting the higher and the lower proportion of MSOME I+II, respectively. MSOME I+II was prognostic for fertilization rate, high-quality cleavage-stage embryos rate, and blastocyst rate. The normality cutoff value based on blastocyst rate was MSOME I+II≥ 5.5%. MSOME could be a useful tool for the diagnosis of infertility severity as it is correlated with sperm morphology, motility, and concentration. Men who had higher MSOME I+II had better ICSI outcomes. The future use of MSOME as a routine method for semen analysis may be a reliable form of assessing male infertility.