Reciprocal effects are due to genetic effects of the parents (i.e. maternal and paternal effects), cytoplasmic effects and parent-of-origin effects. However, in Zea mays L. the extent to which reciprocal effects exist, or can be attributed to specific underlying components, remains an area of interest and study. Reciprocal effects have been reported by several investigators for various agronomic characters in different types of maize materials for grain and silage usage. Maize geneticists and breeders have recognized reciprocal effects as one source of genetic variability, but the lack of consistency in the observation of these effects, particularly due to stress conditions, has prevented a systematic exploitation of these effects in practical breeding programs. There is mounting molecular evidence for underlying mechanisms in maize, which could be responsible for both the existence, and the instability of reciprocal effects. In this study, we developed population of reciprocal backcrosses based on an initial set of recombinant inbred lines. This population was used for dissecting reciprocal effects into the underlying components (maternal, cytoplasmic and parent-of-origin) effects. We also developed statistical framework to identify and map contributions of specific nuclear chromosomal regions to reciprocal effects. We showed that differences in maternal parents, endosperm DNA and maternally transmitted factors collectively influence reciprocal effects early during the season, and that their influence diluted at later stages. We also found evidence that parent-of-origin effects in the sporophyte DNA existed at all stages and played an important role in establishing differences between reciprocal backcrosses at later developmental stages.