Recent fossil finds in China and Argentina have provided startling new insights into the reproductive biology and embryology of pterosaurs, Mesozoic flying reptiles. Nineteen embryos distributed among four species representing three distinct clades have been described and all are assumed to be at, or near, term. We show here how the application of four contrasting quantitative approaches allows a more precise identification of the developmental status of embryos revealing, for the first time to our knowledge, the presence of middle and late developmental stages as well as individuals that were at term. We also identify a predicted relationship between egg size and shape and the developmental stage of embryos contained within. Small elongate eggs contain embryos at an earlier stage of development than larger rounder eggs which contain more fully developed embryos. Changes in egg shape and size probably reflect the uptake of water, consistent with a pliable shell reported for several pterosaurs. Early ossification of the vertebral column, limb girdles and principal limb bones involved some heterochronic shifts in appearance times, most notably of manus digit IV, and facilitated full development of the flight apparatus prior to hatching. This is consistent with a super-precocial flight ability and, while not excluding the possibility of parental care in pterosaurs, suggests that it was not an absolute requirement.