A little studied aspect of developmental arrest (DA) in ART is zygote arrest (ZA). Etiologically, blockage at the first cleavage stage includes molecular and chromosomal anomalies, some of which manifest morphologically. Given considerations on embryo culture, transfer and cryopreservation, optimal zygote selection is very important. The aim of this study was to ascertain whether zygote morphological features were indicators of increased ZA. In this study we performed a prospective, observational study of 2105 zygotes obtained from consecutive patients who were undergoing IVF/ICSI treatment, of which 43 (2%) suffered ZA. Morphological features observed under the inverted microscope were qualitatively categorized: pronuclear size, nucleolar precursor bodies (NPB) alignment, light and dark halos, polar body placement and fragmentation observed at 16–18 h post-insemination. We compared these features in blocked versus cleaved zygotes at 48 h and found significant correlations (p < 0.05) between ZA and three features: the absence of a light halo (p = 0.001), the absence of a dark halo (p < 0.005), and non-aligned NPB (p < 0.05). We can say that certain morphological features are indicators of significantly increased zygote arrest. These findings may be of utility for optimal zygote selection and culture strategies, especially in countries under restrictive conditions.