Studies concerning abscisic acid (ABA) involvement in root system architecture (RSA) and the interaction of ABA with auxin have reported contrasting results. In this study, the effects of exogenous ABA application and withdrawal as well as a combined treatment of ABA with the synthetic auxin 1-naphthaleneacetic acid (NAA) were thoroughly investigated in maize. The results showed that ABA reduced both the primary root (PR) elongation and the lateral root density (LRD), whereas NAA inhibited PR elongation but increased LRD. The combined treatment involving ABA and NAA inhibited PR elongation. Regarding ABA withdrawal, PR elongation was restored when ABA was removed from the growth media, but LRD was not restored after ABA withdrawal. However, the results of the combined treatment showed that auxin can reverse the inhibitory effect of ABA on LRD. A more in-depth analysis revealed that the inhibitory effect of ABA on lateral root (LR) formation depends on the stage of development. Exogenously added ABA blocked the development of lateral root primordia (LRPs) in the early stages, but was unable to inhibit the elongation of developed LRPs. These results suggest that ABA arrests the formation of LRPs rather than the growth and emergence of LRPs and their subsequent elongation.