This dataset contains information on the fertility and physical characteristics of kākāpō (Strigops habroptilus) eggs laid on Anchor and Whenua Hou islands, New Zealand during the 2018/19 breeding season. Of the 252 total eggs laid, 129 failed to develop; undeveloped eggs were dissected, fixed in formalin, and then inspected using fluorescence microscopy at the University of Sheffield UK. For all eggs, data are provided on mother and clutch of origin, developmental stage reached, and maternal mating behaviour. For dissected undeveloped eggs, additional data include fertilisation status, numbers of sperm visible on the perivitelline layer, egg size and weight, dry eggshell weight, and yolk and albumen weights. Full details about this dataset can be found at https://doi.org/10.5285/cd0e9bc1-bd57-44ae-9fec-2f6239e8726d